I did. It wasn't especially difficult at all - but then, the subject of religion was never brought up by the teachers and rarely by the students, so no one knew.

I can easily imagine that it would be difficult in a school and a culture in which public declarations of religious affiliation were accepted and encouraged, even mandated.

I was raised atheist, and it wasn't difficult at all. In fact, I only know the religion (or lack thereof) of one of my childhood friends, which I learned not because he made any statements of belief per se, but rather via his complaints about having to learn Hebrew. As for the rest of everyone I went elementary school with -- we did have occasional critiques of Santa, but it never occurred to me to extol atheism because the topic of religion never came up. When I eventually learned of the great quantities of deluded people around, I had to infer that some of the kids that had never mentioned religion probably were religious, but it didn't seem important enough for me to actually ask to determine which ones.

I don't think I grew up in any great rationalist enclave, maybe my school was just really serious about separation of church and state?

Me neither. My daughter's going to be a test case, though.