What mindstalk said. The few people from Middle Eastern countries who've come out as atheists (usually after leaving their home country) tend to speak out much more against Islam than Christianity. There are a lot of atheists in Israel, and they mostly criticize the Orthodox Jews.

To the degree that atheists are "anti-" any specific religion, it's going to be the one that dominates their environment and stigmatizes them. Atheists in the U.S. aren't usually going to say much about Hindus, for example, because Hindus don't affect them much. It doesn't mean they have any more regard for Hindu beliefs than they do Christian ones.