Even though I grew up in deeply religious east Tennessee, I never understood why people want mandated school prayer. It seems to defy the entire point of Protestantism's dogma of personal relationships with God: If people are forced to pray, well, what's the point exactly? There are no rules in schools that prohibit prayer, so why should there be rules to mandate it? People are always free to say personal prayers to themselves. Even the Bible declares good Christians should retreat to pray in private rather than making a public display of one's supposed holiness.
Kate Sheppard explores a new Illinois law that mandates not prayer per se, but that weird "moment of silence" thing I grew up with part of the time:
It's an interesting case, because it's not requiring students to pray. Well, not exactly. While they're not mandating that the kids pray to any particular god, they are requiring religious observation (even if it's the religion of your choosing) in schools. This is dangerous for precisely the reasons we separate the two in the first place. Kids who don't pray, or whose religious observation might seem weird to other kids, will be ostracized. And teachers are role models, and having them take part in this as classroom leaders will undoubtedly influence children.
Moments of silence aren't exactly dangerous, except in their intent: No one would be so passionate about the issue if it was "just" a moment for silent reflection. Moments of silence are to mandated school prayer what intelligent design is to creationism. I'd actually be pretty behind a secular moment of silence without such an intent. People could pray if they like or simply sit quietly. Public schools aren't the most calming places, but they should be considering their purpose is to educate and create social ties. A mandadtory Everyone Calm the Hell Down Moment wouldn't be half bad.
But this ain't that, which is why it's a bad idea.