Penises are little machines. They pretty much do as they're told, IME, regardless of the will of the person they're attached to. Also, it may take a victim a while to work out that they were actually sexually assaulted, rather than just having bad sex, or regrettable sex. Female victims sometimes tell themselves things like "Well it wasn't rape because he only did it for a couple of minutes" or that it was all just a big miscommunication. Male victims are no different, although the social pressure is on men to portray their own sexual assaults as conquests as opposed to abuse. There's a whole internet meme about it - men tell horrific sexual stories and laugh it off, saying "doesn't matter, had sex".
The image we have of "rape" being about physically forcing someone to have sex while they're crying and screaming and scratching and begging you to stop is false. It's a rape myth. Rape is simply coercing sexual contact with someone else against their will. They don't have to physically resist, scratch and punch and run away for "no" to mean "no". In most cases, for example when you are in a relationship with your rapist, it's a very confusing experience to be assaulted. People are tempted to chalk it up as bad sex, and they're not likely to try to start a fist fight in the middle of the assault.
It's not as hard for women to assess they have been raped because our society views penetration as the thing that is "done" and the penetrated party as the person it has been done to. If you shift your perspective and recognize that sex is something two people do to each other - and receive from each other - willingly, regardless of which bits go where, it's easier to understand how men can be sexually assaulted by women.