As long as he's not interrupting the game at all, I reckon he's free to do what he wish. Of course, if his coach tells him to get over here and get ready for the next play, then he should do that, too. After all, they're there to do a job, first and foremost.
Though it should be noted that last year, the NFL actually penalized a player for praying - that is, a Muslim player. I hear about Christian players praying or thanking god in interviews all the time, but it was a Muslim player who was penalized. Ridiculous. As I recall the NFL went back and apologized for it, but if players can pray, then that means players of ALL religions can pray.