OP, I'm an atheist parent of a 5 year old at a C of E primary school. I understand where you're coming from. We haven't found it easy this year.
I am very reluctant personally to consider withdrawing DS from either collective worship or RE lessons. We live in England but my father's family is from NI and my DM is Scottish so like the previous poster, awareness of the reality of sectarianism possibly colours my view. Knowledge and tolerance for different world views matters a lot to me and withdrawing DS from worship or RE would feel like a step in the opposite direction, rather than modelling the kind of tolerance and respect for different views that I'd want him to grow up with.
However - he was confused, disturbed and upset last term around the Easter story, to the point of screaming nightmares. We feel between a rock and a hard place. I wish RE was taught differently, and there wasn't collective worship. But we're trying to work with the school to find a way through it that doesn't involve withdrawing him. He also doesn't want to be singled out from his peers and collective worship is part of the school's communal life; and I think withdrawal would be made as un-fun as possible, pour encourager les autres.
My advice is talk to the school and inform yourself. We have observed worship and RE (though you have to allow for the observer effect being in play) and have been provided with the lesson plan and collective worship plan for the term, something we will continue to ask for going forward. That way we can be more prepared for the questions and how we'll deal with them. We are just embracing the confusion and the messy diversity of views - being honest with DS that grown ups believe different things and that's OK. DH is pagan, and my DM who he is close to is Church of Scotland, and I'm an atheist, which I guess helps as we already have to cross the bridge at home of the grown-ups having different world views and therefore not being infallibly "right" but respecting each other's right to our opinions. We are very deliberately grabbing every opportunity to talk about other religions at home, linking to what they're doing in RE - so for example, if they're doing "special things" with reference to Christianity, we take the conversation at home onto things that are special to people of other faiths who we know, or what specialness means to me as a non-believer. I am also reading him lots of myths and legends - you can get great children's versions - and we've got the Usborne "Lift the Flaps" books of World Religions. I also recommend a visit (or another visit!) to the Natural History Museum - the earth gallery has a display about the myths that developed to explain earthquakes before people had the science to understand, and I was so grateful we'd visited last summer because when they talked about Creation at school DS was able to place it as "the best explanation people had at the time, before they knew the science" and a myth, and wasn't confused by the disjunct between the Creation story and his knowledge of evolution and geological time. Basically, "chuck information at it" is my solution. Obviously none of that helps when the vicar gets overly graphic in school assembly about crucifixion and your child is waking at 3 am screaming and sobbing inconsolably, but that's it's own issue.
Your local authority will have a "locally agreed syllabus" for RE on its website, which all community schools, Voluntary Controlled church schools and academies which were formerly VC schools have to follow. Your school should publish their RE topic for each term on their website but on a note of caution, our school's website is out of date. The Church of England has recently introduced a more, um, theologically robust way of teaching the Christianity part of RE in its schools called "Understanding Christianity" and DS's school has switched over this year, but its website hasn't caught up yet so their published programme for RE is less hardcore. Best to ask for the lesson plans so you have a clearer picture, anyway.
The RE online website has lots of information about the different approaches to RE, and "why do RE?" which might be an interesting read. www.reonline.org.uk/knowing/why-re/ www.reonline.org.uk/knowing/how-re/ At a C of E or a non-faith school, Christianity won't be being taught as fact, it will be "Christians believe that...". However, in the real world, collective worship is happening in parallel. led by believers, and the children know from that that the teachers believe the truth of the material in RE, so I'm not sure what the "Christians believe" line is really worth.
The National Secular Society has information on its website about religion and worship in schools, and the right to withdraw, which is very helpful and informative. www.secularism.org.uk/education/
If it's any consolation, DS was attracted to the religious stuff in the first term, but the school's treatment of the Easter story has created an instant atheist (to the point that we're actually a bit worried how negative he's become about religion!).