I've been reading a combination of things lately. First, I've been reading a lot of Mennonite history. Second, I've been reading stuff written by crazy people. This led me to a tract written by Theodore Kaczynski, "When Nonviolence is Suicide" (PDF).
Here's some Mennonite history; the Anabaptist movement was roughly concurrent with the Protestant movement, but while the Protestant movement was both spiritual and political, the Anabaptist movement was solely spiritual. The Protestants wanted to replace the Catholics, while the Anabaptists wanted a complete separation of church and state. Because the Anabaptists were nonresistant, they didn't engage in the Thirty Years War, and when the Peace of Westphalia was signed in 1648 it made provisions for religious tolerance ... to an extent. Most of the problem came from the fact that the Anabaptists (which includes the Mennonites) were much more radical in their beliefs than the Protestants, which generated a lot of conflict. And, because the Mennonites were pacifists, they refused to go to war for any reason, even if they were drafted. So the Mennonites, and the other Anabaptists, were put to death by the thousands; easy to do, because they always told the truth and didn't fight back.
Kaczynski's basic point is that there are times - many times - in which pacifism is not consistent with survival. This is pretty obvious. If someone wants to kill you, and you don't have violence as a way to defend yourself, then they'll succeed. There are two situations in which this is not the case. The first is when you have someone to protect you, and the second is when you live in a society in which violence among humans is unheard of. I suppose there would also be a third situation, in which you are so well protected by nonviolent means that it isn't worth the trouble to attack you - like a turtle - but that is a questionable strategy because it relies on secrecy, technological advantage, and requires a large investment.
So if survival is the highest priority, then nonviolence is really more of a guideline than a value. Any values which you're willing to throw out the moment it becomes inconvenient to hold them are inherently without worth. That means that for someone to be truly serious about nonviolence, they must value that above survival. That's why you mostly find strains of nonviolence - of the true kind - in religious people. Survival, in that case, comes second to salvation.
I think this is what bothers me about atheism; the value system seems to necessarily be based on survival. The way they justify that is usually with social evolution. The theory is that we're willing to die for our children because they carry our genetic information, and evolution is geared towards the propagation of genes instead of the survival of the individual. If this weren't the case, lifespans would approach infinity with each subsequent generation. This is all well and good as an explanation of why people are willing to die for somewhat arbitrary reasons, but it doesn't suffice as an explanation for why an individual should die for a non-survivalist cause. That is to say, while we can explain why we might be geared towards martyrdom, that isn't a rationalist defense of martyrdom unless you consider the following of biological imperatives to be the highest aspiration of a human being.