Rabbi David Wolpe, author of Why Faith Matters, makes an excellent point about Religulous:

Perhaps Maher’s greatest misunderstanding of religion is his central indictment: that religion is responsible for the world’s violence. It is not. Violence is a product of human nature. Before monotheism, the Assyrians were not kind; the Romans were bloodthirsty beyond the imagination of religious regimes. When religion became less potent in people’s lives after the French Revolution, instead of making the world less violent, it became far more violent: World War I and WWII, communism, Nazism — all shed blood on an unprecedented scale. None were religious regimes or religious wars.

In fact, Stalin and Pol Pot were both atheists and Hitler was driven by other ideologies. The three of them together were responsible for more deaths than all of history’s religious wars combined. This doesn’t prove that atheists are inherently violent but it does undercut the central premise of Maher’s argument, that our very fate is in danger because of religion.
UPDATE: I’m reminded, too, that the 20th century’s greatest advocates of non-violence — Gandhi and Martin Luther King — were driven by faith.