I'm trying to stay with the original point, referring to male dominance in general, rather than deal with the rabbit trails that lead away from it. The word natural came up in order to confuse that issue precisely because it can be molded to fit any premise.
As to how the word natural came up here in connection with rape, I'm reluctant to put words in someone else's mouth. However, I can suggest that one obvious motive for coupling those two terms might be to find a backdoor means of making rape seem more normal, more understandable or somehow acceptable in some basic, primitive sense. Why anyone would want to find a justification or excuse for rape is beyond me, but I suppose some people feel it's important.
As to the male-female dynamic, it's easy to see that there has been an element of "male dominance" in at least some aspects of the relationship, at least on the surface. But, I don't want to lose sight of the reality that, after all this time, both sexes are still here at the table and both sexes can be pretty tough in the clinches. I'm not ready to declare a winner yet. ;-)