Individual atheists may do evil things but they don't do evil things in the name of atheism.
Give it time. I'm being glib, but not being glib at the same time;) Atheists in great numbers have not been around long. If a country in great power was primarily atheist, and another country that was religious had something those in charge wanted... then we might have a war on religion instead of a war on terrorism. Some might think it is the lesser of two evils to destroy religion completely (by the growing atheist population), rather than allow all the atrocities done in the name of religion to continue - even if there will be casualties of that war. Would all atheists feel the same? No. Would they be drowned out by the angrier voices? If history has anything to say about it, then probably. You can't say that there aren't atheists out there who don't wish that religion could just be wiped off the face of the planet, along with believers. (just listen to some videos and read some comments) Starting of course with the extremists, but movements catch on and, well, before you know it you're in a place unrecognizable from where you began.
If people want to destroy then it isn't going to matter what their religion or their non-religion is. Unfortunately, many people want to destroy, dominate, whatever, to get the things that they want. Sometimes the intentions are good, but those get lost on the way, as well.
Just speculation on my behalf though.
What I would like to point out is that the Christians making wars and dominating other cultures, etc... are NOT following Christ. He didn't want his followers to fight wars in his name.
How can a "true" Christian kill in Christ's name, and do the opposite of what He commanded?
Tammy