It's that way for a reason. The reason being that religion in Eberron is a matter of
faith. It isn't really spelled out for you, least not where I've seen it, but there is a possibility that divine magic doesn't come from the gods at all, but from having faith itself. What you have faith in is irrelevant.
With the presense of godless clerics, one has to ask where they get their power. It comes from the faith they have in an idea or concept. If someone truely worships fire, and has faith in the fire, they will be able to cast from the Fire domain.
Likewise, if you have true faith in a god, you'll eventually be able to gain spells from the domains associated with that god.
From what I understand, the gods are not an active on Eberron. They are very alien. The gods don't grant you spells because you have faith in them. You get spells from some mysterious divine essense (Eberron itself?) simply because you have strong faith in
something. It may be a god, or it may be anything else.
Which makes you wonder..... if spells don't come from the gods, do the gods even exist at all? Which leads us back to the very nature of faith.