Assumptions of guilt and innocence are embedded into how we think about crime. We have a standard way of thinking about that which has served us well on the whole. I think in some cases, that standard position is worth challenging and perhaps adapting. In the case of rape, given the historical context, I choose to make the opposite assumption to what the law mandates in most parts of the world. I do not have any confidence in that assumption, in the same way I don't have confidence in the opposite assumption in many other types of crimes, but I think it's a justifiable starting position to take prior to the investigation.
I don't think that should be baffling, and I'm not baffled by the alternative position. The more you understand about these kind of cases on a personal level, the more understandable my position becomes, IMO.