I can see the benefit for a moment of silence.
It provides a transition from the noisy bustle of the school corridors and playground, and sets a tone for calm in the classroom and readiness to learn.
How the individual child chooses to calm themselves is up to them - if prayer helps them calm down, then it's fine. If meditating on their bellybutton helps them calm down, then fine. As long as the kids and/or teachers who pray don't impose their their manner of "silence" on the ones who use other forms of reflection to calm themselves (and vice versa), I have no issue with it.