There's been occasions in the past (especially on TNG) where religion is treated as something that's pretty much just for babies and humans evolved beyond it. It's always made me a little sad because it just made Roddenberry and by extension Trek seem narrow.
I'm not sure I agree with that interpretation. The primary instance that's seen this way is in "Who Watches the Watchers?," in which the Mintakans' adoption of a superstition based on "the Picard" is talked about as a backward step for their culture. But I don't interpret that as a dismissal of religion so much as a critique of superstition and blind faith, and particularly of using religion as an excuse for violence. When Liko is ready to kill the hostages to try to placate "the Picard," Deanna says "That's the trouble with belief in a supreme being -- you can never be sure what they really want." I can certainly see how that could be taken as a dismissal of religion, but I see it more as a warning against fundamentalism -- saying that you have to be very careful what actions you take in the name of your belief, since you can't be sure whether they're really the will of God or just your own beliefs that you're using God as an excuse for.