When a student or faculty member of a public school reaches campus, they have entered government property. Our government is known to try and follow a simple rule: Do not mix church and state. This avoids controversy, and keeps everyone equal in the law system.
In recent times, it has been proposed that a time for prayer be inserted into the agenda of public schools. This would resemble a moment of silence, or it would be an entire class period during which faculty and students alike could spend time worshiping whichever gods/god/prophet/flying spaghetti monster/tree that they wish.
What would the people in the school who were agnostic or atheist do during this time? Yes, they could stay silent and sit by themselves like the religious people would expect them to, but they would be uncomfortable.
It's like in second grade, when the "popular" and well-liked students would form a club in which only they and the students they chose could join. Whomever was left on the sidelines felt left out. If they didn't want to join the silly game, they still felt pressured to act like they cared.
If a time for prayer is inserted into the schedule of public schools, the constitution will be broken, and those who do not worship will feel left out and pressurized when all of the muslims, christians, catholics, buddhists, pastafarians, and other worshippers go off to do their praying and ceremonies.