While the Constitution does support an individual's right to worship, it also frowns upon the state, or in this case a state-sponsored school, endorsing a religion. Thus, public schools must walk a blurry line between allowing participants to express personal beliefs without those beliefs being attached to the school as an endorsement.
Where's the line between freedom of religion and the separation of church and state? It's a question many cities and particularly public schools have had to ask in the past few months. Most recently, a group of high school cheerleaders in Texas have come under fire for using biblical quotes and banners at football games.