I am in the UK and was quite worried about the compulsory religious education (and it was a bit demoralising that when I asked about it at the open day, they assumed that I wanted lots of religious education and were gushing about how much they did!). However, so far it seems to have actually turned my five year old into a staunch atheist because the bible stories seem so implausible to him. Of course children and schools vary and there are plenty of other reasons to home educate, but so far my fears have been proved groundless in that respect.
I'm also in the UK, and in a similar situation it sounds. I'm atheist, and I'm really quite happy with how my sons school approached religious studies. They covered all the major world religions, and started with hinduism (there are very few hindus at his school, but rather sizeable groups of both christians and muslims - I have a feeling they explicitly chose hinduism to prevent any claims of favouritism).
So when they started learning about religions, my son came home and excitedly told us about Ganesh and Shiva.
But at the end of the entire round, at some point he told me unprompted "I don't believe in god, but I won't tell the other kids, just like with the Tooth Fairy or Santa" (we'd given him strict admonitions when he realised they weren't real to not "correct" the other kids if they come up because some of them might get upset).
Kids spend a lot of time around this age coming to terms with things they believe turning out to be false, and learning to discern them, so in general I think that unless they have a lot of adults actively ganging up and strongly reinforcing something, chances are very good they'll come out not believing.
In fact, I spent more time with my son reassuring him that various real-life things that seems unbelievable to him are actually true (first and foremost, he finds it incredibly hard to believe YouTube didn't exist when I was a kid... I might as well have claimed I had a pet dinosaur growing up; coming to terms with whether or not God is real is apparently far easier than accepting that there was life before YouTube)
