I don't know what goes through an Atheist's mind, but I guess they hate the thought of not being in FULL control of their own destiny. It seems that the notion of (a) God "out there", who would call them to account is too threatening.
The other thing that many of them complain about, and I can fully understand, is that Christians (or any other "religious" person) haven't been the best witness of Who God is, and what He is like.
Atheists are their own gods, whether or not they admit to being so, they are. Anyone who would challenge this would be seen as a threat.