I have no idea what people believed, frankly most kids in my school where just bored by the whole thing and I think you'll find that is still the case with the vast majority of kids. They're not sitting in assembly thinking "God is Great, Allelujah!", they're sitting in assembly thinking "Holy Crap, I've forgotten my math book!" or "I wanna snog Laura from 4D" or something....
They were not indoctrinated, and neither were you. If the education system that teaches you religion also teaches you to question then it's a pretty poor way to indoctrinate someone, don't you think? I think you need to look up what indoctrination actually means because if you accept Assemblies and RE as indoctrination then you need to consider that education in a whole range of subjects from Food Tech to Sex Ed to Sociology to History can all be called indoctrination on some level...