Well you did not lived in the system either, what CCCP had was no true comunism ... it was simply another form of dictatorship.
Comunism is not a evil system, its a utopia that cannot be made a reality because humans are too selfish and corrupted in order for it to work.
And yes I realize why you think that since they pushed religion out as much as they could but that was a stategy based in control, organized religion is a problem to the control of the state since its something they cannot control, in russia case there were other issues since russia was still in medieval age (people still OWNED villages) and was moving into the industrial age, its no suprise there was a uprising against religious leaders as well since they were part of the system (that also happened in europe but not as deep since most of the church autority and power have been sized by the monarchy before the anti-monarcy movements started to take place) and it continued.