Flea, (bass player) from the Red Hot Chili Peppers admits the band WAS NOT playing live during halftime of the big game. There's all kinds of rumors flying that there was lip syncing and Tom Foolery going on. There's even rumors that Denver was pretending to play football! One rumor has been verified, That The Red Hot Chili Peppers DID NOT play their instruments live! The NFL did not want to chance a sound issue botching the whole halftime show, so they made The Chili Peppers record the background track earlier in the day.

The vocals however were 100% live.  Apparently the band was considering not doing the show over the issue. but they decided that it was a "surreal experience" they didn't want to miss. So they went along with the plan. A full statement by Flea can be found here: A Message From Flea