The evils done in the name of religion in general and Christianity in particular is often brought up as a reason not to believe in God. I've never really followed the logic of that.
If someone does something in the name of Christianity that violates the teachings of Christianity, such as using violence to advance Christ's Kingdom (see John 18 v 36), why should that reflect badly on Christianity? Why can we not just see that such actions are contradictory to Christianity's message, and the perpetrators are hypocrites? Would the atheist abandon atheism if he saw a man who said he was an atheist on his knees praying? Would I be justified in saying, "Ha! There you go, atheists believe in God!"? Of course not! The atheist would be quite right to say, "Well that person obviously isn't an atheist, because atheists don't pray!" It would be ridiculous of me to say, "You're not getting off the hook - atheists must believe in God because he claims to be one and was praying!" So it is with the evils done in the name of Christianity - Biblical Christianity can rightly disown them, because such things are against its teachings, and thus such things are no reason to reject the Gospel.
I recently heard an atheist say he abandoned his faith in the Bible because his pastor was commanding the congregation to tithe and when he examined the New Testament he couldn't find a single command for Christians to tithe! This seems completely bizarre, and if you can figure out the logic in that, please let me know. He abandoned his faith in the Bible because a man was telling them to do something the Bible didn't require him to do! But there is no difference in that and in rejecting the Gospel because of evils carried out under its banner.
But for some people it just seems too easy to say that the people who carry out these horrors are not real Christians, or are not acting in accord with Christ's teachings. Again, I don't know why this is hard to accept. The Lord Jesus taught that there would be many people who would profess allegiance to Him, but would not be true believers (Luke 13 v 23-30). It may seem an easy way out, but it is nevertheless the answer to the objection - atrocities carried out in the name of Christ do not have the authority or approval of Christ. Furthermore, to try to spread the Gospel by violence is completely a non-starter, because the Bible teaches that people are not Christians by undergoing a ritual or observing an ordinance, but by genuine repentance and true faith in the Lord Jesus - you cannot force someone to do that! You can force people to say they've done it, but what good is that?
It has to be said that the atheist has no such easy way out, because atrocities carried out by men who were motivated by their atheistic worldview are not one bit inconsistent with atheism - how could they be? Atheism tells us there is no objective standard, no transcendent law, no supreme court or Judge. Their moral outrage isn't founded on atheism, but founded on the fact that they are made in God's image with the work of God's law on their hearts (Romans 2 v 15), and they can recognise good and evil.