"I like your Christ; I do not like your Christians. Your Christians are so unlike your Christ."
The above quote is of disputed origins. While commonly attributed to Mahatma Gandhi, it can neither be traced back to him, nor does it seem to fit his all-inclusive philosophy. Nevertheless, whoever the quote actually belongs to, it has an excellent point: Christians, no matter how hard we try, are very much unlike our Christ.
The fact that we are so unlike our Christ makes it so very strange when unbelievers use us to criticise Him, and the faith He has established. Nevertheless, they do this often. Whether they are judging the actions of an individual, a group, or even an entire culture, they never stop to ask "is this because of Christianity, or because of humanity?"
Christians do not claim to be superhuman. We are distinct from the rest of humanity in only one way: Our standing with God. In all other ways, we are the same. We still have bodies of flesh and blood. We have our individual strengths and weaknesses, just as all others do. Most importantly, we still sin. If any so-called Christian claims to be without sin, our own Bible tells us he is deceiving himself, and the truth is not in him (1 John 1:8). Because we sin, we are a terrible benchmark by which to judge Christianity (if it even made sense to believe you could judge Christianity by its morals).
A large portion of moral objections to Christianity are actually objections to humanity. Things like war, slavery, discrimination, and various other things, do often involve Christians, and yet, we see these things in every culture throughout history. Ironically, Christians are often at the forefront of stopping these things, yet this is not used to show Christianity is good, so where is the logic in using them to suggest it's bad? In reality, the closest you can get to pinning some evil on Christianity is showing that it is somehow compatible with it. And I don't mean in the "this verse could be interpreted that way" kind of way. I mean showing that, contextually, the evil fits with Christianity.
For example, let's take Luke 19:27: "But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me." This verse is spoken directly by Jesus, and is used by atheists, such as Sam Harris, to try to suggest Christianity commands violence against unbelievers. Ok, how many people did Jesus kill? Contextually, this verse is the end of a parable, which begins at verse 11. If Sam Harris and his ilk would back up a mere 16 verses and read from there (which we can safely assume a fair few of them have), they would know that not only is this a parable (i.e. a non-literal story with a deeper truth the reader is required to think about), but it actually ends up saying the exact opposite of what these unbelievers want it to say. If you believe the Bible is true, you know that Jesus is speaking about a future event, namely Judgement Day, when unbelievers will be justly judged according to what they have done. It is not a command to Christians. If you don't believe the Bible is true, you don't believe this event will ever happen, and so even if you are so illiterate that you believe this is a command to Christians, you believe they'll be waiting for ever before they have to carry it out.
Now, does that mean no one claiming to be Christian has never killed someone else for religious reasons? Certainly not. Christ Himself was crucified at the hands of those who claimed to follow Him (keeping in mind the doctrine of the Trinity). But Christ Himself neither commands, nor does He even allow, the killing of unbelievers. Christianity is a religion of peace, even towards unbelievers. But lethally violent sectarianism is a very human problem. Because it is a human problem, it is a Christian problem. No one claiming to be a Christian, even if they murder for sake of their religion, should be used to judge Jesus, nor the faith He set up.
Ironically, there is a flip side to all of this. Whereas unbelievers are quick to pin certain evils on Christianity, they are also quick to show that there are Christians alive even today who support evils they approve of. Rather than use this to suggest Christianity is untrue (which, of course, they still believe), they will instead use this to claim that these evils are somehow compatible with Christianity. Take, for example, the increasingly popular practices of homosexuality and abortion. It is said that because there are Christians who are supportive of both of these, and even those who practice them openly, they must therefore be compatible with the Christian faith, and therefore, either Christianity is false because it evolves at the whims of the culture, or at the very least conservative Christians (i.e. those who believe the Bible) are just being dinosaurs, clinging to dying ways. But the answer remains the same! Yes, there are sinners who claim the Christian faith, but these are not Jesus, nor do they have authority to alter the Christian faith.
Therefore, this argument, whichever perspective it approaches from, is void. In all of history, only one man has ever walked the earth by whose actions one could judge Christianity. That man, of course, is Jesus, and we, as Christians, are to imitate Him (1 Corinthians 11:1). When we fail, that's entirely on us. Therefore, judge Christianity based on the God whose name it bears.
But be warned; at the end of the day, it is not you who stands judgement over Christianity, but God who will stand judgement over you. Just as Pilate discovered, when you judge Jesus, you will find no sin. Jesus did not kill. Jesus did not rape. Jesus did not discriminate. But perhaps you will still find Him "guilty", as you are a sinner, too. What that means is you commit evil, and approve of evil. When you judge Jesus, you may well call Him evil, because He commands that which you hate, and condemns that which you love. But in that case, you are wrong. You are the evil one, not Jesus, and just as your sin causes you to hate Him, it also separates you from Him.
Yet as much as you hate Him and refuse to be reconciled to Him, He loves you, and seeks reconciliation in the most dramatically good way imaginable. Rather than punish your evils as He ought, Jesus' perfect life ended on a cross, receiving your punishment. Therefore, through faith, you will receive eternal life, adopted by God as His son or daughter.