Actually, I think social dynamics and hierarchy in men's prisons are very relevant - they are a world without women, after all. It's not such a reach to think that a man with propensities for rape that may have been perpetrated on a woman outside would be perpetrated on men inside. It really is not about sex.
It's not talked about a lot, but many men who would not identify as gay do form loving relationships with other men inside (human needs for love, comfort, companionship, sex), and have to deal with the whole gay stigma after they get out. Anyway my point there is that inside a prison not all sex is rape.
So... is it worse for men? Speaking about male on male rape, I agree with the Rapscalious one, depends on the person. In terms of society, it's also totally subjective what "worse" means. Women deal with not being believed, having their character assassinated, being told that they caused it because of their appearance, on and on. Men have to deal with a challenge to their sexual orientation, a challenge to their maleness, a smackdown re: their standing in the pack - note that all of these things relate to social hierarchy. Then, they also have to deal with the other awful things women go through.
It makes me think that on some level, women are already at the level in society where being raped doesn't interfere with their social hierarchy (unless they live in a culture where they *must* be a virgin before marriage). So maybe from this point of view it is worse for a man, because he's fallen further since he was up higher to begin with.