While you're right that the vast majority of fantasy (high and/or epic) employs a monarchy of some type, I don't think it's nearly as prevalent in science fiction as you seem to imply. There's countless examples of ruling councils, federations, presidents and the like in sci-fi. Plus, if you include urban and paranormal fantasy in your sampling, I think you'll see the monarchy's stranglehold take a sharp nose-dive in fantasy as well.
If it's "historical" in its setting (milieu, whatever), it's really kind of natural that a monarchy's going to be tapped for the governmental model more often than not (but I certainly appreciate it when the "nots"
do occur.
)