Even in a world where the gods can be proven to exist, it doesn't necessarily follow that the gods will be worshiped. It is still possible to simply treat the various gods as little more than ultra-powerful spirit beings. None of the gods, as traditionally portrayed in D&D, are omniscient, omnipotent, or omnipresent. In such circumstances, both atheism (by believing that the so-called "gods" are just another intelligent species) and monotheism (by believing in a spiritual principle that transcends to so-called "gods") are both possible.
In many ancient beliefs, the gods aren't treated as personified natural forces, but rather individual beings that happen to have particular interests in different natural forces. Many different goddesses, for example, could be interested in Love, but none of them is actually the force of Love itself. One prayed to a god to get them to use their magic powers on your behalf, but the fact that you could pray to the god meant they were a personal being, not an abstract force. If anything, the traditional conception of gods in D&D has been exactly in line with the attitude I've just outlined. In such circumstances, it is entirely probable that different races and cultures will prefer dealing with different gods, and certain gods will prefer to deal with certain races above others.
In my own campaign I include atheistic Philosophers who can do everything Clerics can do, but explain it as being done by hypnotism, reasonable deduction, and knowledge of the vibrations that underlie reality. They can even turn and destroy undead in their presence, because "ghosts don't really exist". My campaign worlds have always tended to towards the idea that the gods either didn't really exist at all (and clerical miracles were really just a variant form of magic), or were actually Chtuluesque monstrosities that pretended to be gods to play games with lesser intelligent species.