Update: When I first drafted what follows, I gave substantial credence to the view that Devin P Kelley was an atheist who repeatedly expressed hostility toward religion. As it turns out, those reports were highly exaggerated and it appears that his motivation for his murder of dozens of people in a church is far more likely to be part of "a domestic situation". Kelley has a long and awful history of domestic violence, against women, children, and animals.
I leave what follows as I originally wrote it (except for fixing some typographical errors and perhaps adding some references. I believe that it is a valuable commentary even if the specific incident that motivated it isn't applicable to the point.
We already know that someone who commits mass murder isn't right in the head. This is true whether they are nominally motivated by global Jihad, defending the unborn, protecting the white race or instigating the uprising against the Fascist state. It is no more or less true when it is motivated by a hatred for religion.
So what should my fellow atheists do when one of these atrocities is committed by a self-professed atheist, who appears to have been motivated by his hostility to religion in general and Christianity in particular.
We can correctly point out atheists do not call for violence against believers and that most atheists believe in freedom of religion, and fully respect the rights of people to believe. There is no way that this killer was taking cues or hints from "the atheist movement" (to the extent that such a thing exists).
We can correctly point out all of signs of mental illness in the individual that are distinct from his atheism or atheism in general. But that applies equally well to any of these other kooks. If I criticize some aspects of religiosity for the horrors brought by the religious, I shouldn't expect to hide behind "he is a kook who doesn't represent us" even though he is a kook who doesn't represent us.
We could even try to say that no true atheist would do such a thing, as we value life, reason, and human dignity. This would be a stretch in the best of cases (as atheism and humanism are not the same things even if many atheists are humanists). But I would not accept that argument from religious people who use it to avoid looking at how their own belief system may have supported some of the craziness of the killer. So I won't accept this argument here either.
Are we (atheists) doing something wrong?
So is there anything about atheism or the atheist community that can be legitimately said to contribute to the kinds of awfulness we've seen? I'm going to say that there is a little something that we should try to correct, but that it is tiny compared to responsibility that religion and some political ideologies have to bear for what crazies do in their name.
Atheists, for the most part, do not really care what other people believe. A Christian might be highly motivated to change my mind about things in order to save me from eternal damnation, but I have no equivalent motivation to change a Christian's mind. We merely think that believers are wrong about some things. We don't believe that their error is part of some evil demonic force (because we don't believe in such things). And we certainly don't believe that we have God on our side.
It is true that most of us probably believe that the world would be a better place if people were less religious. And so there is scope there for caring about what others believe and disliking those beliefs. It is possible in these terms to imagine some sort of ideological crusade against religion. Perhaps that was part of the motivation, but on the whole, you don't see atheists even talking about trying to suppress or punish religious belief. You see us trying to persuade.
Uncomprehending insult
But despite that enormous asymmetry, I do think that there is a little something that we could be better about. There are substantial portions of the atheist community and online communities that paint believers as sheep, cowards seeking comfort, weak-minded, deluded, infantile, mentally ill, and other unpleasant things. This is because we struggle with understanding how (otherwise) reasonable people can believe things that to us are patently nuts. We really do struggle with that question.
The problem is that we genuinely do not understand this facet of the majority of our fellow humans. Now I have my theories, but this isn't the place for them, but most of guesses spouted by many of my fellow atheists to not paint a pleasant picture of believers.
It is easy to think poorly of people we disagree with, particularly if we can't really understand why they disagree with us. It's clubby to ridicule them. It makes us feel special and superior. Now this is fine to an extent. It's like what Longhorns say about Aggies. It becomes a problem if we take it too seriously. And it becomes a problem if the dangerously disturbed among us take us too seriously when we talk in those terms.
I don't know if that kind of talk played any role in this particular case, but I do think that we atheists should make an effort to remind ourselves and each other that the large majority of humans are decent and (otherwise) reasonable people just like us.