So the question is, how strong do they think those gods are?
To those in the know, who've cracked the system and worked out that the gods are only as powerful as the belief they engender and that they are pretty much forced to comply with how they are believed to be, these atheists are scary dangerous.
So they believe that the gods are arbitrary and evil, likely to meddle in the affairs of men for no reason, to nobody'l benefit. So if enough of them believe strongly enough, that'll start to be true. Then they'll get more believers, etc etc etc. Ragnarok.