A common attack atheists launch against the Christian faith is to point out the large number of mutually exclusive denominations. Because they are mutually exclusive, they cannot all be right, but they can, at least logically speaking, all be wrong. Sometimes, they'll throw in the occasional curve ball and suggest that a truly omniscient and omnipotent God wouldn't allow His followers to fall into such confusion.
There are many ways to answer this objection, of course starting with the simple fact that it isn't a necessary conclusion. "You can't all be right, therefore you're all wrong" is a stupid argument, and any atheist who makes it should hang their head in shame. Even adding "God wouldn't allow this to happen" shows a shocking ignorance of both the God of the Bible, and the mankind of the Bible.
Which brings me to the way I most like to answer the objection. Pure Christianity requires three crucial elements: Faith, knowledge, and integrity. If any one of these three elements is weak, it will almost inevitably lead to a weakened version of Christianity.
Faith
Faith is the first crucial element. This is a belief in that which one cannot actually see. I can see my laptop right now. Of course I can. That's how I know the words are actually appearing on screen as I hit the keys. But when I go out to the cafe, or take my dog for a walk, of go to church etc., I can no longer see my laptop. I have faith that it hasn't randomly caught fire and burned my house down, that my dog hasn't jumped on it (again), or that no one has broken in and stolen it.
Our faith determines not only what we do, but also what we say. If you believe the Bible, you're going to act like it's true, and preach it as if it's true. By contrast, if you don't believe it, you're not likely going to let it shape your life, or even preach as if it's true. Think of it this way: If an atheist knows what's in the Bible, and is willing to act perfectly consistently with what he believes, he still will not preach the Christian faith.
Knowledge
Knowledge is slightly more fixed than faith. This is the belief in what one has experienced directly. We know, for example, that the sun exists, both because we can see it, and because by its light, we see everything else. As an interesting side note, a man born blind must place his faith in the sun, because there is no real way for him to verify its existence.
If a Christian believes that the Bible is true, and is willing to act on it, that doesn't make a difference if they don't know what it actually teaches. It is worth noting that, in stark contrast with the claim that God "would not allow" confusion, most Christians throughout history, when they study His word, have come to some very similar conclusions.
Integrity
Integrity is perhaps the most important element, because if you believe the Bible is true, and know what it teaches, but have some kind of interest in it not saying these things, you're still not going to give an accurate representation of Christianity. The obvious problem here is that according to these same Scriptures, we're all sinners at war with the Holy God.
If any one of these three elements is faulty within a person, they will both possess and exhibit a faulty version of Christianity. The problem with this is that every human being on this planet (yes, myself included), is weak in each element to some degree. I have faith, but sometimes I have doubts. I have knowledge, but it's not like you can walk up to me and say "hey, what does 1 Kings 3:7 say?", and have me answer "Now, O Lord my God, You have made Your servant king instead of my father David, but I am a little child; I do not know howto go out or come in." (Which, coincidentally, is Solomon asking God for the knowledge element). I have integrity, but I can still be tempted, and do still sin. And there isn't a single human being, with the sole exception of Jesus, who has ever walked this Earth who can say otherwise.
This simple fact renders the argument from sectarianism completely impotent. If anything, because it so perfectly displays the nature of human beings in exactly the way the Bible describes it, the existence of various denominations is fantastic evidence for the Bible. But it's interesting to note that it's not just atheists who use this argument. There are several sects within Christianity whose apologists, rather than claiming "they can't all be right, therefore they're all wrong", will say "they can't all be right, therefore we are".
We can immediately dismiss the Mormons when they argue this way. Other than being a brand new sect of Christianity with a brand new book, shinier than the mythical golden plates it was supposedly translated from, they follow a man who was notorious for being severely lacking in the integrity element. Obviously you cannot come along 1800 years later, make up a bunch of fanciful tales about the hidden history of the continent you live on, and claim to be the sole correct denomination just because there are large numbers of denominations that did the same thing before you did.
But it's actually a very old trick. From the very beginning of the Christian faith, Satan has been setting up fake Churches to either deceive, or at the very least harass the real one. In fact, a lot of the New Testament is specifically designed to rebuke these false teachers, and correct the Church for accommodating them. With statements like "You have become estranged from Christ..." (Galatians 5:4), or "For if he who comes preaches another Jesus (...) you may well put up with it!" (2 Corinthians 11:4), it's clear that fake versions of the Christian faith have been floating around since before God even delivered His final Scriptures.
Although it cannot trace its origins back to the Apostles, the Catholic Church is a very early group of heretics, going back at least as far as the Edict of Milan in 313 A.D. Much like atheists and Mormons, Catholic apologists frequently point to the large number of "Protestant" denominations (which is their code word for "everyone who isn't us") to suggest that the Bible has failed. They of course will not use those words, as they believe the Bible is the inspired word of God too, but they do claim that the Bible, contrary to its own claims, does not make the man of God complete, and thoroughly equipped for every good work. Thus, we need their help to determine what it says.
In an effort to prove this, they often go to the so-called Church "Fathers". A Church "Father", according to Encyclopedia Britannica, is "...any of the great bishops and other eminent Christian teachers of the early centuries whose writings remained as a court of appeal for their successors, especially in reference to controverted points of faith or practice." It includes, to name just three, Clement of Rome, Ignatius of Antioch, and Augustine of Hippo.
The primary reason Catholic apologists go to the so-called Church "Fathers" is, I believe, mainly because they know that while most Christians have Bibles, they very rarely study the Church "Fathers". Thus, it's an easy fight. "Oh, you didn't know Ignatius taught a literal transformation of the bread and wine into the real body of Christ? Well, now you know the early Church taught the Catholic version of the Eucharist, and not that corrupt version Luther made up 1500 years later".
In my experience, Catholics tend to get quite sheepish when it turns out the Christian they are debating knows a little more about the Church "Fathers" than they would like to. In reality, no one has a monopoly on these men. Sometimes, they held views similar to Catholics. Sometimes, they held views any "Protestant" would immediately recognise as our own, even using the same arguments to defend them. Sometimes, they held views no Catholic or "Protestant" in the modern day will affirm. But the truth is, it doesn't matter what the Church "Fathers" believed, because just like us, they were men who had their weak points in faith, in knowledge, and in integrity.
But still, the Catholic will argue, they were closer to the Apostles than we are, so shouldn't we trust them? As one Orthodox believer I once debated put it, "Imagine thinking you can interpret the Apostles' writings better than the people who listened to them preach live, face to face."
From a fleshly perspective, this makes a certain amount of sense. If the Holy Spirit is removed, humans are generally better at understanding the people we've met than the ones we merely admire. I, for example, greatly admire William Tyndale for his valiant efforts to bring the Bible to the laity, in spite of violent (and, for him, fatal) opposition from the Catholic Church. But since I never met him, I can't exactly claim to know him as well as his friends and family could.
But there are two problems here, the first of which being this Orthodox believer is simply adding to the number of interpreters. Rather than me going to read the Bible, he wants me to interpret his interpretation of his Church's interpretation of the Church Fathers' interpretations of the Bible. That doesn't sit well with me, for obvious reasons. But setting this aside, when we do read the Bible, what we find is that even God's chosen vessels were not perfect in faith, knowledge, or integrity.
Doubting Thomas
To begin with, we have Thomas. This man is so famous, we literally call people who are overly skeptical "Doubting Thomas" after him. Thomas was a personal disciple of the Lord Jesus Christ, accompanying Him throughout his ministry. Much like the other disciples, Thomas not only saw Jesus' miracles, but in some cases, was given these powers himself (Matthew 10:1-8; Mark 3:14-19).
In spite of having seen these great things surrounding Jesus, Thomas is famous for having doubts about the resurrection. When he was told by the other disciples that they had seen Him, he refused to believe it unless Jesus personally appeared to him and let him put his finger in His wounds. Now, of course, this did actually happen, but until it did, do you think Thomas, even being a faithful disciple of the Lord before the crucifixion, would have run around preaching "Christ is risen"? This is the central message of the Christian faith, and yet a disciple of Christ doubted it until Christ personally showed up.
Now, imagine for a moment we could find Thomas' personal diary, and it read "I can't believe it. Jesus did so many miracles. He healed the sick. He cast out demons. He fed more than 5,000 people with a basket of fish and bread. But He's dead. It's over. Peter's not handling it well. He says Jesus is back. I'll let him have his imaginary friend for now and hope he gets over it." What should we do with such a find? We should take it as being of historical interest, but we know that not even Thomas believed it in the end. Should we not, therefore, do the same with the writings of the "Fathers"?
Ignorant Saul vs. Hypocritical Peter
Before he became an Apostle of the Lord, Paul was named Saul of Tarsus, and he was notorious for persecuting Christians, even to their deaths. After his conversion, Paul later testified to Timothy "Even though I was once a blasphemer and a persecutor and a violent man, I was shown mercy because I acted in ignorance and unbelief." (1 Timothy 1:13). Here, Paul demonstrates that he once had both a lack of faith, and of knowledge. He did not know Christ had risen. He didn't walk with Jesus during His ministry. In fact, being a Pharisee himself, if Paul ever met Jesus prior to His resurrection, he was probably among those who tried to kill Him. Even this seems unlikely, as Paul would be expected to comment on his prior experience with Christ if, indeed, he had any.
But setting aside the question of how much experience Paul had with Christ prior to His resurrection, we can be 100% sure he did not have as much as Peter. Nevertheless, in Galatians 2, we find an incident where Peter falls short in integrity, and it is Paul who corrects him: "Now when Peter had come to Antioch, I withstood him to his face, because he was to be blamed; for before certain men came from James, he would eat with the Gentiles; but when they came, he withdrew and separated himself, fearing those who were of the circumcision. And the rest of the Jews also played the hypocrite with him, so that even Barnabas was carried away with their hypocrisy. But when I saw that they were not straightforward about the truth of the gospel, I said to Peter before them all, “If you, being a Jew, live in the manner of Gentiles and not as the Jews, why do you compel Gentiles to live as Jews?" (Galatians 2:11-15).
Note, Peter is not being straightforward here. This is an accusation of hypocrisy. Peter knows the truth, and believes the truth, but is not acting in accordance with it. Now, if Peter was a full grown heretic, he could easily have turned around and said "what, you think you know Jesus better than me? I knew Him before He went to the cross. You didn't even believe He rose again until He collared you on the road to Damascus." But of course, Peter wasn't a heretic, and is now enjoying his eternal rest at the right hand of Christ. Nevertheless, according to Catholic logic, surely "Pope" Peter has more authority than Paul? So who is Paul to rebuke Peter?
Judas Iscariot
Much like the other disciples, Judas Iscariot was very close with Jesus. Though of course he is infamous for his betrayal of the Lord, he nevertheless had no different status from any other Apostle during Christ's ministry. He was still given the same power and authority, he was sent out ahead of Jesus with the same message, he saw Jesus' same miracles. The only real difference between Judas and the other Apostles came after His crucifixion.
Judas, of course, had no integrity, nor did he have faith. We are told, in no uncertain terms, that Judas would have been better off if he was never born (Mark 14:21), and that he was a devil from the start (John 6:70). This tells us that Judas is a Hellbound sinner who should not be imitated. His proximity to Christ did not matter. It didn't save him, and it won't save you.
Why this all matters
All of these Biblical examples demonstrate, to some degree or another, a certain weakness in faith, knowledge, and integrity. Some of them, like Peter, are still, for lack of better term, the "good guys". It's just that they weren't Jesus. They weren't perfect. They made mistakes, and we should not imitate those mistakes, but instead learn from them. Others, sadly, are "the bad guys". They didn't just make a bed of errors, they now lie in those beds forever. And unless you want to lie in those same beds, you do not want to imitate them either, no matter how close they were to Christ.
The Bible warns us that we should have the same attitude towards the Church "Fathers". Aside from the obvious potentially false teachers among their ranks, even the good ones are not perfect. Therefore, they are not a valid test of Scripture. Rather, we should use Scripture, i.e. the word of God, who is perfect, to test their words. When a Church "Father" says something Biblical, we should believe them, but only in the same way as we believe our own pastors when they say Biblical things. When they say something unBiblical, like Jesus was 50 when He died, or the Jews are circumcised so they can't get to Heaven, or having sex with your wife too often is adultery (all real Church "Father" beliefs), we can reject them because they disagree with the Bible.
The conclusion of all of this is that it really doesn't matter how divided the modern Church is. As long as the Church is made up of human beings, it will be filled with Thomases, and Peters, and Pauls, and even Judases. And we won't even always be in the same state. Sometimes, a Paul might become a Thomas. other times, a Thomas may become a Peter. A Peter is in serious danger of becoming a Judas. And occasionally, by the grace of Almighty God, a Judas may well become a Paul.
So, what exactly does sectarianism prove? Answer: Precious little. As I said, it may be evidence for the truth of Scripture, as Scripture accurately describes the nature of man and the state of the world, warning us that there will be both false teachers who make fake Churches, and even good men within the Church who, at least on occasion, will fail. The existence of denominations, therefore, does not help the atheists. It does not help the Mormons. It does not help the Catholics. It doesn't even help the Liberals, who are a different kettle of fish altogether.
But this might leave us with one final question: Which denomination is the correct one? Actually, none of them. Denominations are a carnal construct. As Paul says, "And I, brethren, could not speak to you as to spiritual people but as to carnal, as to babes in Christ. I fed you with milk and not with solid food; for until now you were not able to receive it, and even now you are still not able; for you are still carnal. For where there are envy, strife, and divisions among you, are you not carnal and behaving like mere men? For when one says, “I am of Paul,” and another, “I am of Apollos,” are you not carnal?" (1 Corinthians 3:1-4).
These denominations, much like any other carnal thing, should not exist. They do exist, for the same reason as Christians who watch porn, or steal from their mother's purse, or covet their neighbor's house, or lie etc. But they shouldn't exist. They do not please God. If they did, God would have given one to us. But He never did. Instead, He told us to avoid them like the plague. He's given us community in order to preserve His word, and build each other up in our pursuit of it, but He didn't say "ok, this Church over here, this one has all my doctrines right, so lump the book itself, just follow them and they'll steer you right." No, He says "All Scripture is given by inspiration of God, and is profitable for doctrine, for reproof, for correction, for instruction in righteousness, that the man of God may be complete, thoroughly equipped for every good work." (2 Timothy 3:16-17).
So really, there are no true denominations. But... there are true Christians in denominations. You may have heard the phrase "the Church is an organism, not an organisation". This saying reflects the fact that, ultimately, we are all children of God, the body of Christ with Him as our Head, not because we follow some super-Church, but because we are saved by one common faith. Many denominations deny that faith, but the irony is, most "Protestant" denominations are united on it. We are united to the extent where a Baptist believer may fellowship in an Evangelical Church, or vice versa. It all comes down to having the truth Jesus, the true Gospel, and the true spirit. If you have these things, your denomination does not matter. There are true Christians in every denomination, but there are no true denominations, and it is a sign of spiritual maturity to recognise that.