This is tricky and I feel very much the way you do as to regards to religion.
My son goes to a school that is based on Christian principles. It is really hard to find a school that isn't. They do discuss Easter etc and they pray before the eat and I must say it doesn't bother me. We do not discuss religion at home or pray. Sometimes he prays at home when I give him his food and it is actually really sweet. If he chose a bible in the shop I may buy him one, reluctantly.
He is still young, but when the time comes and the questions come, I want him to understand that there are different religions and that he should be informed.