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Prayer neccessitates a religion. It is based on the idea you have something to pray to.
Which means that you want to force any kids I might have, to pray to something they are going to be raised to not believe in.
The state does not have that right and a teacher in a classroom is an organ of the state, the teacher is not there to spread religion, even if it is religion in general, the teacher is there to do their job.
Teachers can still be religious, they can still pray they can still organise prayer meetings - they just can't do it using state resources. Public schools are state resources.
Note how the legislation does not apply to private schools, which can be religious, because they are not state resources.
What you are whinging about, in essence is that the state isn't allowed to shove religion down student's throats - something you guys accuse atheists of because we write the odd occassional book.