I know that it's different a bit for me since I'm from the UK, but my old school was a non-religious school (and indeed we had a sizeable number of Muslims and Sikhs in the lower years when I left). Nevertheless, we had a formal group prayer every morning during our school assembly. There was no problem if kids didn't join in, one of my best friends was a staunch atheist, whereas I'm Christian (non-practicing though). I'd join the prayer, my friend wouldn't, and a lot of the non-Christian kids wouldn't join in either. But the teachers were fine with that, and the school was especially tolerant of all races and religions.
Therefore, from my own personal experience, I'd say it's down to the school itself if they want to include prayer, but they shouldn't be allowed to force it on everyone. If a school wants to include prayer in assemblies or whatever then nobody should have the right to prevent them from doing so. So I disagree with most posters so far. Nevertheless, if someone decides they don't want to join the prayer, they shouldn't be forced to either. Tolerance works both ways.