A while back I spent some time reading up on female-on-male rape. Apparently most of it involves the guy being asleep (either naturally or due to being intoxicated/high, or drugged by the woman), and he comes to with the woman riding his cock and still being too out of it to throw her off.
Beyond that you've got your blackmail/coercion/sexual harassment situations, and the old gag where the room is dark and she pretends to be someone else in order to have sex with him.
Actual female-on-male violent rape would have to be very specific circumstances, a woman highly trained in combat skills could probably pull it off with an out-of-shape guy with no fight training.
The overwhelming majority of rapes in general are done with drugs. More on topic, a fairly recent study
found that about 18% of men surveyed reported that a woman had raped them using force.
Your last paragraph goes a ways towards explaining why it's so underreported, in that you imply, if not directly state, that every
man is stronger than every
woman, and that only a trained martial artist could possibly overpower a man. Feeding into the belief that any man who's raped actually wanted it.