This is exactly what we have debated in another thread about judging. This is exactly what Jesus was talking about when he invited the one without sin to throw the first rock at the prostitute. This is exactly what Jesus was talking about when he said that we should yank the log out of our own eye before complaining about the speck in our brother's eye.
Some Christians have been responsible for their own atrocities, it's true: The Crusades, the Inquisition, the political pandering, the coersion of the powerless into accepting the "state religion" of Christianity. Some of us scream the loudest when slaves wanted to be freed, when blacks wanted equal rights, when women wanted equality, when homosexuals want equal treatment under the law. I would be willing to bet that many of the Christians who are yelling the loudest about how evil Islam is, are the very ones who would have opposed emancipation, women's suffrage, and equal rights. They subscribe to the same kind of over-zealous, narrow-minded, draconian sort of religiosity that the Muslim extremists subscribe to. It's all terrorism -- the Christian version is just a whole lot subtler and more subversive...and not as many cars get blown up. But judgment and demoralization sometimes are worse than fear and destruction of property and life.
Not all Muslims are evil and depraved. Neither are all Christians! Some Muslims and some Christians work ardently for justice, for peace, for unity. Some Muslims and some Christians believe the best about people and hold hope for humanity. It's not naivete, it's a choice. We peacemongers don't have the wool pulled over our eyes -- why do you think we work so hard for peace?!? But what we don't do is what I see happening in this thread: we don't generalize and assume that, because the evil is sensational, it must be ubiquitous.
You Christians who say, "Islam is as Islam does" need to remember American slavery, cross-burning, the silence of the Church during the Holocaust, the Inquisition, Apartheid, Northern Ireland, and the Christian President who turns a blind eye to prisoner torture. You need to remember that the world looks at us and says, "Christianity is as Christianity does." If you don't want to be seen as hate-mongering religious extremists -- if you don't want Jesus portrayed that way through the actions of his followers -- you -- then you need to stop worrying about the speck in the eye of your Muslim neighbors and concern yourselves more with the log in your own eye.
You atheists need to stop using these atrocities to blame the religion. Instead, blame the people and hold them accountable for their own deplorable actions. Hold them accountable to the the religion to which they claim adherence.