The Pardoner is a character who is ruthlessly honest with his fellow travellers about his job and how he tricks people. Although he says nothing that shows he is an atheist, and doesn't believe in God, it is clear that his approach to religion is that is something he can use and abuse in order to make money. Note what he says in his Prologue to his tale:
Because my only interest is in gain;
I've none whatever in rebuking sin.
No, none! When they are pushing up the daisies,
Their souls, for all I care, can go to blazes.
These words are very unequivocal about the Pardoner's approach to God and religion. They are merely tools for him to trick the gullible so he can make money easily and not have to work. He pretends to be somebody who "rebukes sin" whilst in reality is only interested in exploiting those who don't see through his deception. This shows that he cares little for God, though it does not literally state he does not believe in God completely.