Huggy's right in that 'ism' denotes a system. That system is theism. The prefix 'a' is negation. So, 'atheism' literally means 'not-theism' just like 'amoral' means 'not-moral' in the sense of being not connected to/involved with those things rather than in a pejorative sense (which would be 'antitheism' and 'immoral' respectively).
Aside: moments like these are why my calls for certain people to go back to school are 100% serious.
Aside: moments like these are why my calls for certain people to go back to school are 100% serious.