This is an old post, but worth linking to now regardless. Alonzo Fyfe at the Atheist Ethicist makes this important point.
If you take “atheism” and its counter-part “theism” NEITHER of these are a source of violence or evil. You cannot draw any moral implications from the statement, “It is not the case that at least one God exists” just as you cannot draw any moral implication from the statement, “It is the case that at least one God exists.” They are both behaviorally, morally, and practically impotent.
In order to get to any moral conclusion – any type at all – you have to add something to your fundamental premise, regardless of whether it is atheist or theist.