Flipping the question around, how often are D&D characters going to experience a modern, judeo-christian perspective on what a god is? I'm seeing a lot of that perspective here, but I'm hard pressed to think of a world where the same events came to pass. (Granted, it's theoretically possible, but with big-outsider gods, how likely is someone to develop a theory of an inaccessable, omnipotent, modern-style god?)
So I'm seeing little basis for D&D athiesm in a standard campaign, simply because their definition of the word "God" is miles away from ours. Attitudes from blase apathy to outright Athar-ish "damn meddlesome things ruining it for humanity", would probably filter down from the more powerful adventuring types, but that would depend on the actions of gods and religions.
Granted, the perceptions and actions of religious institutions (in any world with D&D style gods, there will be those devoted to worshipping them, athiest population or no,) could be a whole seperate (although intertwined) issue, but that's a debate for later...