There is the Purity Legion Enforcer prestige class from inner sea combat. They are required to be atheists. They are also granted several anti-divine powers, like better saving throws against divine spells, the ability to detect divine spells and holy paraphernalia, and the ability to sever the connection between a divine spellcaster and his deity with a critical hit (basically shuts down all their spellcasting for several minutes). It is hard to see this as anything but atheist as a class. They even have an ability called Iron-Willed Atheist (Su) which grants them spell resistance against divine magic, they are literally canceling out the power of the gods with their lack of belief.
Logical (or at least playable) reasons to be athiests are easy. What do you call it when you know of the gods but don't worship any of them, and have no faith or even are opposed to faith in general. Many would call such a person an atheist.
What even makes a god special in a world with dragons, demons, and meteorites that can make gods out of random drunken humans. remember a human can be turned into a god in pathfinder, so why are gods special other than power, which many things in pathfinder have. The sliding scale of powers makes gods lose their awe and specialness. so why worship them.
Fantasy atheists can come in many flavors. some of these are more atheist than others, but most lack faith which is the basic requirement.
Some people are just offended by the idea of relying the gods instead of trying to fix things on your own. They will succeed or fail on their own merit, they see prayer as giving up. To them whether the gods exist or not is basically meaningless.
"Do not pray, when you pray your hands close together and you can no longer do."
You have the people who acknowledge that the gods exist but don't think worshiping them makes any sense. They have no faith to speak of. They don't worship the gods for the same reason they don't worship the local king or the powerful mage, they do not see it as a worship type of relationship. This tend to be very egalitarian types of people. They follow their own conscience and if the gods don't like it that is their problem. The gods are just another powerful thing in the universe, nothing special. What exactly is the difference between a really powerful demon, dragon, or mythic character. This would be completely compatible with the Purity legion enforcer.
"There was no difference at all between the richest man and the poorest beggar, apart from the fact that the former had lots of money, food, power, fine clothes, and good health. But at least he wasn’t any better. Just richer, fatter, more powerful, better dressed and healthier. Gods are the same, just becasue the gods have power does not mean I should worship them."
Some just don't want anything to do with the gods, thinking involving yourself with them invites trouble. This is probably the least athiest of the list, but they may well be common in a fantasy setting.
“You don’t bother gods, and gods don’t come bothering you.”
Some are just mad at the gods for doing what they see as such a piss poor job of running the place. They may believe in the gods but they do not respect them. More importantly such a person may deny the gods just as an act of rebellion even if they do believe in them. The Purity Legion Enforcer often falls under this, seeing gods and/or their worshipers as detrimental not beneficial.
"If I meet god in the afterlife, he's going to have a lot to answer for."
Alternatively there are those that see religions as intentional or unintentional tricks. Keep in mind in pathfinder the gods do very little directly, so who is to say the gods are not just a powerful energy source the clerics have tapped into and are not just making everything else up. This is another group that plays well into the Purity Legion, and also could be type 2 at the same time.
“I remember in your Citadel I saw a crowd stoning a man to death in a pit. Ever seen that? Don’t know about the soul. All I know is, it was a horrible sight. Oh, I’m not talking about the poor bugger in the pit, I’m talking about the people throwing the stones. They were sure all right. They were sure it wasn’t them in the pit. You could see it in their faces. So glad that it wasn’t them that they were throwing just as hard as they could.”
Followers of a more hands off type of god may never invoke them at all in terms of anything but the occasional curse by them. their god is not an interventionist god and they have no problem. in this case telling a believer from a non-believer is all but impossible.
"I do not pray to him, he does not listen, he gave men courage and wisdom and it is up to us to use them."
Some people just don't care. The gods just are not important to them, they have more direct and practical concerns.
"No, offense but you have to much time on your hands if you can worry about that, I got fields to plow, hogs to feed, and a leaky roof to fix. Unless your god is going to come down and help, you can keep em'."
Then you have people that just absolutely refuse to think in new way or look at the world in a critical manner and just believe the first thing they were told for their whole life. They exist everywhere, and in our world are morel likely to be religious than atheist, but that is just due to numbers, and the fact that with science not-supporting gods it just makes the religious ones easier to spot. In a world with gods then the a-religious ones would be easier to spot.
--Insert close minded quote of your choice