Carrie:
He kills off everyone in a prom who constantly make fun of a Christian girl -- but the one's who are her friend or try to help her do infact survive.
Desperation:
The only atheist is a really stereotypical prick with no care for anyone else.
1408 (short story):
Man is tormented in a room for his lack of belief.
Battleground:
Atheist is tortured by a bunch of toy soldiers.
Children of the Corn:
Atheist couple are attacked by a bunch of crazy kids and one is killed.
Pet Sematary
A non-practicing family loses their son.
Dead Zone:
A man who disobeyed his Christian mother about gambling was forced into a coma for 6 years.
--
It's undeniable. This man hates atheists with a passion.