As an atheist myself, having had religion rammed down my throat as a child, I didn't want to subject my sons to that same treatment, so I had them removed from RE classes.
Then, when my younger son was halfway through Year 10, his school called me in and said that even though I'd removed him from these classes, he still had to sit in the same classroom and that it was MY responsibility to provide him with alternative learning for these sessions.
My son told me not to worry about it because by being made to sit in the same room, no matter what he might be working on, he could obviously still hear (in his words) "the rubbish the teacher was spouting" and would actually like the opportunity to voice his beliefs because she was only covering Christianity and nothing else. So by his choice, I officially put him back into the lessons.
The teacher didn't like him saying that there were more religious (and non-religious) options available than just Christianity and she complained to the head teacher, who called me into school and I referred him back to my son. At the end of the year the teacher left the school.
Year 11 rolled around and I went to parents' evening in October and spoke to the RE teacher who told me that her mother was Muslim, her father Jewish and that she herself was Atheist! She told me that she taught the subject holistically, based on the premise of people of various different religions believing different things and that my son would be encouraged to include his beliefs (or lack of) in class.
This new teacher was an absolute breath of fresh air, so much so that when exams and results came around, to my astonishment and sheer pride, my son actually achieved an 'A' grade, basically because he'd followed this lovely teacher's way of dealing with the subject and stating in his answer to the first question on the test paper that he is Atheist and on the subject in question his beliefs were abc, people of other religions might believe jkl or xyz, that there was no right or wrong as to their choices but that we are all human and have the right to believe whatever we choose and should all respect the rights of others to choose for themselves too!