I went to a religious school when I was in kindergarden (age 3 to 5). I didn't make much of it, because other issues were more important. I learned very little about religion at that time, like the story of Moses's life and a few celebrations. At the same time, my parents at home kept telling me there was no God, so by then I used to think God belonged to "the other" religion. Not very effective as you can see. Back then I also used to think that half the people were Jewish and the other half were Christian.
My primary and secondary schools were secular. My background and beliefs were not an issue there, except for an incident with a girl in first year of secondary school who had been raised in an antisemitic family and tried to make my life a hell.
Then most people at university have been strongly atheistic, to the point that some of them laugh at people who believe that souls exist by themselves rather than as a result of physical and chemical reactions. Others just raise an eyebrow and say "ah, right, you're one of those". I've often felt uncomfortable in such situations. And, of course, many people believe that religion is inherently bad, and the cause of most of the world's evils.
Fortunately, I can think for myself. Which has led me to disagree with just about everyone (perhaps literally everyone) I know as far as beliefs are concerned. But I don't really mind, as long as people respect other people's views and don't try to force them to change.
As far as education goes, I think it's good for children to know about religions (different religions, if possible, and I'm including atheism here because I've seen that atheists can be as radical as the most religious), and to be given the chance to decide what to believe rather than being forced. I don't know how feasible that is, but I think it would be the best option.