There is a big difference between Muslims taking time to do their own thing, and prayer before a 'state-sponsored' football game. The first is an individual's right, and does not affect anyone else. The second is seen as a 'state-sponsered' religious activity.

The way I see it, the state should not sponsor or set up any religious activities in schools or elsewhere. I also think that each student has the right to read their Bible or whatever, and pray in their spare time at school. The distinction being an individual's choice vs. a sponsered event by a governing body.