I guess anything that happens in nature can be described as natural, but I think what some people here are suggesting is that rape is not a very successful strategy for succeeding in our natural world. It's not hard to find people who think that rape is the natural order of things - just visit any maximum security prison. But their view of rape is a minority point of view and most societies dispose of or segregate people who think like that either before or soon after they begin trying to spread their genes around. ;-)
It's kind of hard to say what 'natural' means isn't it? But that vaguely defined new-agey word seems to have reached an ascendancy over more prosaic and scientific words like 'historically.'