Let me make something clear. There are ways on the atheist side of keeping things civil. Before I ran into new atheists I had many, many, respectful discussions with nonbelievers, and that includes passionate nonbelievers. What I have noticed, and it's something I trace back to Dawkins, is a shift in the nature of the discussion. I remember being surprised by it in a couple of discussion groups I got into before I even opened this blog. There are people on the other side who see the disagreement between belief and unbelief to be not just a debate but a war, and who want to mobilize a people who use ridicule, not in a offhanded way, or a way that is aimed at entertainment, but aimed at providing people with a social, not an epistemic, motivation for abandoning belief based on fear of ridicule. This ridicule is not for the benefit of the believers they are debating. They are written off as hopeless. No, it is used as a tool to demotivate religious belief amongst the low-information believers in the flock, who might be influenced by "naked contempt." Your debating partner is a pawn in a game, the end justifies the means.
Now, it is quite true that Christians have not always, historically, been willing to leave an open marketplace of ideas and have not always treated nonbelievers fairly. How Christians got to the place where there were willing to use the power of government to uphold their beliefs raises some difficult questions. I think the lessons of history have taught Christians, the hard way, that using force on behalf of one's beliefs is a self-defeating enterprise.
Violence on these matters is only possible when it looks to us as if our cause will benefit from it. Even if I decide that Dawkins is the worst influence on society possible, it would be silly to kill him, that will prove his point on a number of issues and benefit his cause. But even if that were not the case, it would violate the teachings of my religion to kill him. That was an important part of my point, that the failure to engage or not engage in violence is partly a function of what one sees as useful, and this is true of both theists and atheists. One response to the recommendation that the Pope be assassinated in the name of atheism would be that it doesn't work. But that better not be the only reason.
I am willing to ask anyone who thinks whether one believes or not really matters, what means they are willing to use to get people to get the right answer. The charge I am responding to is the charge that RELIGION leads to violence. The road to violence, however, is open to everyone. I think, if anything, Christianity has some safeguards that limit the damage, which may be why, as Dinesh D'Souza points out, the death tolls are actually lower in the religious cases. For Christians, it is hard to argue that the end justifies the means, that the course of history is really in our hands. My claim is that you get ideological violence when you have the power to commit it, when you think the end justifies the means, and when you really think it will benefit your cause to commit it.
When I hear that religion is a mind virus, when I hear that everything depends on curing that mind virus, then I have to wonder what means are NOT acceptable in achieving that goal, should the opportunity arise. That is the basis of what I said here.