As my Grandfather always said, "2 things are to be avoided in polite conversation. Religion, and Politics." and I think to exclude Gods and Religion from D&D cuts out something that to me, is very interesting.
My mom adds a third: Sports.
Anyways, my take in religion is a mix of Greek mythology (or how I interpret it), the Dawn War take on religions, Eberron's take on religions, and the Athar's philosophy.
In my campaigns, the gods are very real beings (because I like gods as fantasy characters and feel that a fantasy world without gods lacks in the fantasy department), but they are most of the time distant from the mortal world. Sure, they can appear in the mortal world some times and do naughty word there before returning to the Astral Sea, but most of the time they are focused on cosmic stuff, leaving mortals on their own. The fact that my gods are powerful beings on their own right that don't need worship juice to exist and their powers aren't tied to the number and intensity of the faith of their worshipers (an FR/Planescape bs I don't like because I feel is stupid) means the gods are less interested to be involved in the affairs of the mortal world and no need to force mortals to worship them or else you'll end stuffed on Atheist Hell/Wall (another really stupid idea). When they do it is because they want to do it, not because they are forced.
This allows for a setting were people knows there are actual gods out there but the gods doesn't enforce their wills on them, and when mortals commune with the gods they can't fully understand them (because mortal minds cannot fully comprehend cosmic stuff). Which means an Eberron-like status were mortals must find their own answers about the nature of the divine, and so there are a lot of churches, cults, sects, beliefs, heresies, etc., allowing for the focus of the campaign to be on the actions of the faithful rather than the doings of the gods. My take is also pantheistic/henotheistic, so people worship many gods at the same time, like praying to Bahamut for protection, Avandra for good luck, and Bane for victory in the next war. Some people will have a preferred (read patron) god, but is not common and not enforced.
This also allows players (and even NPCs) to be atheistic in the Athar's way. After all, there is no way to confirm if the gods are actually the creators of the cosmos and worthy of worship, or just extremely powerful beings that happen to be worshiped by easily impresionable people.
And this doesn't contradict the fact that sometimes the gods can (and will) intervene actively in the world and start events and the like. But when they do it, they remain focused in the stuff that interest them and nothing else. Like in the Iliad, when the gods were very interested in the Trojan War, taking sides, manipulating events, and even directly intervening in the fighting, but the rest of Greece was left to their own devices. And once the Trojan War was over, the gods returned to Mount Olympus and left the mortal world to fend for itself (save for poor Odysseus, but he deserved it and Poseidon just focused on him).