Eh, they did do an episode taking on scientology. That takes guts, because those guys are litigious as fuck. I haven't seen any other show attempt to take them on and I imagine South Park's episode about them provided a lot of insight for people who didn't know just how bizarre their beliefs are.

On the other hand, you're not wrong about them straight-up calling some people "dumb." Their episode explaining Mormons literally sings, "Dumb, dumb, dumb" throughout the story. Yet even that episode was honest - Joseph Smith did claim to use a seerstone in his hat to read off golden plates. (Apparently there was a treasure-hunting fad going on at the time, where people used "seerstones" to try to find hidden things. Joseph Smith already had experience with that, and he scryed for treasure the same way he "read" the golden plates - by putting the stones in his hat and attempting to see through them.) They were also right about Lucy Harris and how Joseph Smith reacted to her. Athough Matt and Trey inserted their opinions through a voiceover song, they told a pretty accurate, educational story.

They do occasionally miss the target terribly (those earlier global warming denials frickin' hurt), but they mock a lot of celebrities for more than being "a dumb person." Kanye's mocked for his massive ego. Bono's mocked because the creators think he's a hypocrite. George Lucas and Steven Spielburg were portrayed raping a storm trooper, as a clear metaphor for how Matt and Trey thought they were violating and destroying their own work.

I don't agree with some of their accessments and choices, but they do tend to attack a lot of other characteristics than just "dumbness."