I didn't realize the "atheists-are-jerks" meme extended all the way to conflating atheists with MRAs. Atheism and feminism are (often) tangled up in one another. A wonderful source of misogynistic justification is to be found in any holy book you wish to point to. Atheism usually throws this out, along with feminism, and to some extent this sympathy is very strong. I suppose you could imagine a darwinian atheist believing that women have biologically enforced traits that make them somehow "lessers" to men, but I can't think of anyone, ever that has expressed this idea in the modern era (some 20th century authors having a derogatory view of women aside; this was "normal" from any ideological perspective at that time.)
You haven't noticed the evolutionary psych reasons MRAs give for their misogyny. I do not want to do that research for you because gross. Edit: This question -- are misogynist trolls atheists or Christians? -- is an interesting one. Misogyny is cooked into many religions, but unfortunately, the ethos some people take out of "survival of the fittest" isn't always awesome, either. I looked at Elliot Rodger's manifesto (again, gross), and he definitely is not coming from a Christian place. According to him, he, Elliot Rodger, is an angry God (ahhh, mental illness...), and women are animals. He uses the word "species" at one point, but there's no clear indication that he thinks Charles Darwin wanted him to do it.