Well so we can find more common ground, let's approach it from a different perspective.
Granted there are Islamic and Christian fundamentalists who espouse violent means. Do they do this only because they are fundamentalists? No. Do they do this only because they are Muslims/Christians? No. Do they do this only because they are theist? No. Do they do this because they are theist, Christian/Muslim, and fundamentalist? Not completely. There must be other social, economic, or political considerations when explaining the roots of the violence.
True, people have fought "in the name of God" and gotten others to fight alongside them. People have killed for heretical deviation of doctrine. True, all of these instances cannot historically be unlinked from politics. Blaming all this killing on theism is not a good thing.
Take it a step further. I hope you will agree that not all religions are theistic. There are atheistic religions. Religion does not require belief in a creator God. Such religions have been involved in wars. But we cannot attribute the violence to atheism.
So we all know that one need neither be a theist nor an atheist to engage in violence. However at this point, one could still argue that religion causes more violence than secularism. Religion, more accurately competing religions, makes groups and individuals susceptible to violent behavior. An organizer can appeal to religious grievances and mobilize an armed force. That same organizer can also use ethnic differences, tribalism, economic exclusion, nationalism, among many other things. Violence often occurs with these other things, and without the presence of religion. Yet there are no or few calls for the ending of ethnicity or tribal or all economic structures, even though ethnic or tribal or economic disputes are often the "cause" for violence. Instead we hear calls more often for peaceful coexistence, dialogue, political action.
Degrees of exclusion, isolation, difference, belonging to a group, social structure in any form are the real "root" of violence in the sense that the New Atheists mean. Violence is human. It's been here before religion, before monotheism, before atheism, before everything. Violence is, in a sense, natural and not exclusive to any belief or disbelief.
Now, when people here say "Atheists" a lot of the time mean those who advocate the primacy of human reason, science, and secularism. For better or worse, those things are becoming the characteristics of a group. It remains to be seen what it will do if it's ever as a group, singled out for something like economic repression, ideological cleansing, political fault line formation, etc. All hypothetical and unlikely, but the hypothetical capacity for group structure and ideology formation is there. Though these hypothetical malcontents may not use the battle cry "for atheism!" they could use something like "for rationality" "for science" "for demystification" or something that the atheistic trait is only a part of.
I don't think this will happen, but I don't think any group is impervious to the temptation or justification of violence.