I am not sure if this has been brought up before, but some atheists like to blame Cristianity for much historical violence, such as anti-semitism, the plight of the native Americans, the Crusades, the religious wars of the 1600s, etc. I am not sure how to respond to it. Sure, people in the Church made mistakes, and some were guilty, but many were not. Seems like there is some steretyping and scapegoating going on.
When people turn to such arguments it's actually a giant logical fallacy. This is why I find books by Dawkins, Hitchens, et al
to be worthless because most of their arguments are purely illogical. Their fallacious nature is also not a formal fallacy, where the structure of the argument is flawed, but a material fallacy where the conclusions they draw from the argument are flawed (thus rendering the argument and/or conclusions false).
The argument, "Christians caused the Crusades, therefore Christianity is false" is the fallacy of composition (this is the first of many fallacies in this argument). It assumes that something in the part reflects upon the whole. So we say, "John is a boyscout and John hit that old lady. Therefore, all boyscouts like to hit old ladies." While that might be true of John, it certainly isn't true of all boyscouts.
When I am faced with this argument, I generally turn it on them and say, "80% of the prison population in America is African-America. So this must obviously mean there is something wrong with being African-American that causes you to commit crimes, correct?" This almost immediately begets a response of, "Of course not!" to which I say, "You're right! But the logic of the aforementioned bigoted statement is the same logic you use against Christians." I mean no offense by the example used, merely to show the danger in the atheist's logic.
Other atheists will look past composition and simply argue that Christianity was the cause
of the Crusades. But this also brings about the fallacy of questionable cause. Just because A seemingly causes B doesn't mean that A is the cause of B. For instance, were Christianity the cause of the Crusades, then we should see other evidence of Christians performing Crusader-like actions throughout history - that is, peaceful Christians should be abnormal. However, the opposite is true. What we see - especially in the first three hundred years of Christian history - are a people who border between quasi-pacifist and fully pacifist. Furthermore, to defeat the cause argument one could easily point to not only the early history of the Church, but also to the Scriptures themselves and the teachings of Christ to see how the Crusades - though militarily and politically necessary (the First Crusade at least) - contradicted Scripture.
Of course, the same above test can be applied to Islam or atheism to see if they are the cause of violence. In the case of Islam, the answer is yes. In the case of atheism, the answer is far more ambiguous. Not all atheists have allowed for warfare, however, there's on "stop-gap" to speak out against violence in atheism, at least no justifiable way to do so. To be fair, in order for Marxism to succeed (as a true form of Marxism and not some neo-Marxist mentality where religion is co-opted rather than attacked), it has to adopt a materialistic view of the universe (i.e. atheism). But this doesn't mean that all forms of atheism would support a Marxist view.
Regardless, the argument, "Christianity has killed people!" is an empty argument as there's no logical basis to said argument. Furthermore, as many others have pointed out here, there is egg on the face of everyone in this instance.
Finally, I might add, the Orthodox suffered under the Crusades and did not invoke the Crusades.