First off, mainstream bad. Remember, Radiohead is still more popular than Muse have ever been, and though a lot of garbage is played on radio, the fact that it's played on radio is not the reason it's garbage; there are plenty of great mainstream acts, like Lily Allen or (dare I say it? On the internet?) Kanye West.
Second, every indie band and their dog was on the Twilight soundtrack. I bet almost everyone on this message board has an artist on that soundtrack they'd say they like, from Thom Yorke to Bon Iver to The Killers to Grizzly Bear.
As for Muse's new album itself, the Resistance I'll admit that I didn't like it as much as Black Holes and Revelations or Absolution; however, it didn't suck because they wanted to appeal to more people. (their sound appeals to surprisingly diverse tastes anyway.) It wasn't as great because they tried to follow up on their progression in sound that was on Black Holes, but the album just didn't have the same drive. There are a lot of new directions in the record, some interesting grooves, and it's overall pretty good, but it doesn't have the same energy their last records had.