hmm... I hadn't thought of it before, but I suppose it kinda is a fairly common trait in the adult games I've played. Some of it is just cultural weirdness, I presume. for instance, there are a lot of scenes in japanese adult games where the girl says a LOT of "stop" and "no", but the context of the scene was a consensual and mutually desired sex scene... something that occurs so often I sometimes wonder if good japanese girls are just expected to say that kind of thing regardless of consent, as if it would be unladylike to be enjoying anything sexual. I have no hard evidence to support that, it's just a theory I have based on the media I've consumed, so treat it for the rumor mongering it is.
Even putting that aside, however, there is a lot of unambiguous rape in japanese porn games. Like, I absolutely love the unbridled zaniness of the Rance games, but geez, dude...
As to why that is, well, there are a variety of schools of thought that look at psychological and sociological foundations behind kinks, including rape fetishism and dom/sub and the like. I'm neither qualified nor interested enough to offer a properly informed opinion, but the general consensus of others is that sexual media depicting fictional rape/domination scenes are popularly consumed by a fairly large portion of individuals of both genders, that the media generally appeals to different psychological aspects of the people viewing it for reasons outside the act itself, and that the vast majority of the people who do indulge in those kinks are not rapists, nor likely to become such.
...which is all fine and good, but it doesn't do a lot to help those of us who want to play the occasional nukige but who don't have a fetish for that kind of thing. XD