Short answer: It was cancelled.
Long answer: A change in management at the SciFi channel in 1998 led to someone who hated MST, Bonnie Hammer, being put in charge of programming and they immediately declared season 10 (which hadn't gone into production yet) as MSTs final season. The reasons given were that the show was somehow effecting the networks profitability, but MST was actually one of the most cost-effective series on TV at the time (pretty cheap to produce, good ratings, tons of built-in fanbase, guaranteed audience for home video releases and licensing). It was also suggested that the rights to the movies was too expensive, but this has since been debunked since the movies were, like in the case of Comedy Central, movies that had already been licensed in large packages for the network already and MST was just choosing from the bin, so to speak. (viewers of the Sci-Fi channel during these years might even remember that a few of these flicks were already showing as their weekend movies, including, embarrassingly enough, Quest of the Delta Knights) MST negotiated for a few years of re-runs and some of their defenders still within the network snagged them a spot on the SciFi website to do Edward The Less (which was not renewed for further seasons, obviously), but that was pretty much the story of that.

Was Bonnie Hammer the one responsible for the SyFy rebrand?

I found the fact that they got 3 years of reruns on the same Saturday morning timeslot that they had, and they only made new episodes on SciFi for three years, and only showed less than half of those episodes within that three year span, and still must have paid out royalties for those reruns. I dunno, it always seemed oddly personal when it came to the SciFi axe.

Bonnie Hammer. I always figured it would have been Joe Don Baker.

Bonnie Hammer was basically the entry point for USA Networks to directly run the channel, as opposed to SciFi just being a division of USA. And yes, it was all part of the re-branding to eventually become SyFy. They were hurting a lot money-wise in the late 90s because of all their dumb gambles on terrible in-house programs and made for TV movies that were awful.

Oh, and basically MST being cancelled was because she didn't like the show personally. All of that said, it's unfortunate that after the cancellation Jim Mallon went to such lengths to try and prevent the MST folks from making money on anything remotely related to MST. (he then took over the full rights to the name and made those astoundingly terrible MST web-cartoons and then threatened to sue Mike and crew for trying to do The Film Crew) As far as I know, only Mallon, Hodgson, and Kevin Murphy still make any money off the royalties because he knows, legally, he can't NOT pay them, but he managed to boot everyone who was not a founder of Best Brains out of getting any paychecks.