What do Catholics and atheists have in common? Both use the large number of denominations as an argument to prove their case. For the Catholic, the alleged 30 - 60,000 Protestant denominations is enough to prove that Protestantism is wrong. For the atheist, the 30 - 40,000 Christian denominations is enough to prove that both Protestantism and Catholicism are wrong.
In both cases, the argument has enough flaws to make me need to remind myself that I am a Christian, and calling people stupid is against my religion (Matthew 5:22). Arguments, on the other hand, are fair game, and so I have no qualms about saying that this is a very stupid argument, for a number of reasons.
First, the figure itself is hugely exaggerated, as is proven by the fact everyone who uses it cites a different figure. Needless to say 30,000 and 60,000 are quite far apart. That's 30,000 denominations that get missed! The actual figure is somewhere closer to 1,000.
Second, as is shown by the difference between the Catholic and atheist version of the argument, it doesn't work because you can simply add your own denomination to the list. Catholicism is considered to be a Christian denomination, so why should Catholicism be true and the others false? "We can't all be right, therefore I'm right" just isn't an argument. The same applies more broadly to atheists, who not only make this argument with regard to Christian denominations, but religion in general.
But the most glaring error in the argument is that once you cut out all the blatantly heretical denominations, such as Mormonism, the Watchtower, and, yes, the Catholic Church, a denomination effectively becomes a "big name for a little difference". In other words, actually, yes, they can all be right, at least when it comes to the Gospel.
At this moment in time, I have a particularly funny Family Guy cutaway gag in my head that illustrates the point perfectly. Two Christians, a Methodist and a 7th Day Adventist, meet in the street and randomly discuss their religious beliefs. The Methodist randomly explains that he believes Jesus is our savior, "and we remember Him by going to church every Sunday." The 7th Day Adventist replies "we believe all the same things that you believe, but we go to church on Saturdays." The Methodist has a cartoonish freakout, eventually bouncing down the street away from the 7th Day Adventist, and the cutaway gag ends.
Now, I have heard that 7th Day Adventism is a cult, with many strange beliefs aside from the Saturday worship, so I wish to clarify that I know next to nothing about the denomination, and neither is it relevant for the moment. Focusing entirely on the gag as an example, "I believe all the essential doctrines of Christianity, but have this minor difference from your church" is enough to consider a Christian church to be a different denomination. However, the core of the faith is still the same.
Think of it this way: A Lutheran, a Baptist, a Methodist and an Evangelical could all feel perfectly at home in each other's churches. The church I personally attend is an Evangelical one, but our pastor came from the Church of England, and my mother is a Baptist.
It gets better, because even in the heretical denominations, there are actually true Christians. This is because not only is a denomination a big name for a little difference, but you don't even have to commit to a denomination. There are some denominations that will excommunicate you if you don't believe what they tell you, but most denominations insist on one central book: The Bible. Members of different denominations can worship in each other's churches not because we prefer specific hymns, have a specific method of baptism, prefer certain ways to take communion, host services on specific days, or any other tiny differences, but because we all have exactly the same Scriptures.
Although different denominations may have different opinions on what the Bible calls "doubtful disputations" and tells us not to argue about them (Romans 14:1), the Bible has the advantage of having been written down, which means when bigger disputes show up, we can go to it to find out God's final word. Where God says "yes", no denomination can afford to say no. When God says "no", no denomination can afford to say yes. When God is silent, Christians are free to agree to disagree.
Back when Bible Brain was still God Squad Apologetics and Path Treader Ministries, I had four admins: Carl (me), Styx, Layla, and Sammie. Sammie, at one point, identified as a Lutheran. However, when we discussed this topic in more depth, she told me she hops between denominations, generally just identifying with whatever church she attends at the time. She has since told me that she no longer identifies as Lutheran.
When I issued a poll in another ministry, I asked the question "Out of curiosity, do my Christian audience identify with any specific denomination?" Styx added his own option: "Somewhere between evangelical, baptist, non-denom".
My answer was simply "no". I don't identify with denominations, neither do I call myself "non-denominational" (which is, as Tim Hawkins says, basically just "a Baptist church with a fancy website"). Although I attend an Evangelical church, my personal view is that denominations are a waste of time. As long as the Bible is available to me in a language in which I am fluent, I don't need a church to teach me. Furthermore, whenever a church does try to teach me something, I hold it accountable to the Bible, and reject whatever the Bible disagrees with. Or, as I say, "let the Bible judge your denomination, don't let your denomination judge the Bible."
Layla's opinion has been influenced by me. She agrees with my take on denominations, but believes denominations are somewhat useful for telling you what an individual believer does, or at least is likely to believe. Last time I asked, she identified as "Bapticostal", a blend of Baptist and Pentecostal, which I am told would be an adequate description for my beliefs. But of course, barring the heretical denominations this ministry is designed to rescue people from, the most I know about most denominations is their name.
And so we see that denominational differences are not an argument against any particular denomination, "Protestant" denominations, or Christianity as a whole. Whether or not a denomination is true is not dependent upon whether or not there are other denominations, but how much it adheres to the Bible, and (just to satisfy atheists), whether or not the Bible is actually true.
The most important thing the Bible describes, which all true denominations believe, is that the Lord Jesus Christ was born of a virgin, lived a perfect life, died on a cross and rose again. Through nothing but faith in this, and the confession thereof, we can be reconciled to God in spite of our sin. Any denomination that denies these facts, whether there be one or 10 trillion, is false.