Personally, I've never really found the idea that Tom Cruise might be secretly gay to be particularly funny. Mostly it just reminds me of the guys passing him on the street in Eyes Wide Shut calling him a faggot--it just seems kind of immature, and provoked by the fact that he's handsome, but not as particularly macho as other pretty leading men of his generation.
But I do think it's stupid how angry he gets over the jokes, which may also be the real point of the South Park episode. And I do agree with Stan's assessment of his acting ability--I don't think Cruise is a bad actor, but John Heder probably is a little better.
As for the Scientology stuff, Matt and Trey really seemed to be just phoning it in. It's not as funny as the Hubologists from Fallout 2--the South Park episode basically relies on actual facts of Scientology to be funny by themselves. Matt and Trey used to be more inventive. I wish they'd retire, before the show shares The Simpsons' fate.