In Russia's case, in addition to being one of the few characters you might mistake for a 'bad guy', it's probably the getting-way-too-physically-familiar habit that he has. I'm thinking also of France and Italy as other characters who get closely intimate, and France has this problem with getting cast as a rapist, too. Italy... is too busy being a fanon uke to be a rapist. It's probably not the fact that he's a virgin.

Germany isn't presented as a 'bad guy', and he's more on the physically reserved side.
And so the stars aligned to cast Russia as rapetruck, and Germany avoided most of it.