My thought is basically this: when Darwin wrote his thoughts on Natural Selection, he wasn't at all interested in how things should be, but more in how they actually are. The strong will survive, and the weak will eventually be weeded out.
While I agree that Nazism certainly took some kind of hint from Darwin, I don't think Darwin himself had any interest in creating supermen, or eliminating the weak in society (though, looking at 19th century thought, I wouldn't be surprised if he was into eugenics or something like that).
I think an atheist would probably say that, for whatever reason, humans have a deep aversion to the suffering of their own race. It's an instinct that can be repressed, but, in general, we don't like it. This instinct developed and survived in us as a product of evolution, and so the causes of social justice don't necessarily conflict with the idea that weaker traits and species are eventually eliminated by nature. Even if they did, I think most people are fairly averse to the idea of "helping evolution along." If it's true, it's going to continue regardless of what we do to help it or try and hinder it. Just because we don't like it or think it's potentially damaging doesn't make it untrue.
The main problem with atheism is that it works entirely with borrowed values. As a system, it cannot on its own produce a way to call some things good and admirable and desirable for their own sake, and others evil and punishable for their own sake. To all "moral" statements (even the idea that progress is good), they must attach the disclaimer, is you will, that it is a "human instinct" or something like that.
What ends up happening is that atheists end up having a similar "morality" as Theists (except for the part about about everything being about God), except instead of morality, they just call it instinct. The problem is that instinct cannot carry with it moral obligation, but most either have never thought that far (your average HS atheist/agnostic/whatever), or else ignore it.
Honest atheists ought to be nihilists.
Although it's debated hotly, many people (including yours truly) believe that the Third Reich's ideas about a "superman", master race, and all that was them taking evolutionary thought to a logical destination.
I think, though, in general things are more complicated than that. I am quite certain most atheistic evolutionists don't think that we should ignore the poor in the interests of a more straight path for evolution. And I'm sure there are evolutionary theorists who believe that care for the least of these is one aspect of evolution's path (i.e., it's part of what moves the race forward).
I dunno. But I do think Darwinism in many of its forms (social darwinism, for example) permeates our thinking.