The problem most people have (including egyptologists) is the lack of religious understanding. Akhenaton was not a monotheist in the true sense. He was what is referred to as a henotheist. This is the belief in many gods/divine beings with one of them being supreme. he possibly believed in monolatry, which is that there is more than one god, but only one should be worshipped.
Not to get off topic, but I've always been of the belief that Akhenaton did away with Amun worship for political and financial reasons. Think about it, he does away with the powerful Amun cult and seizes all their holdings, while at the same time elevating the Aten to the supreme god, the only one to be worshipped/donated to, with him as the central figure. Actually quite a brilliant strategy imo.