The impression I got from Trek is that humans from Earth are past religion. Note Pcard's early speech in Who Watches the Watchers
TNG could be insufferably smug at times about the things humanity had supposedly "evolved" beyond needing, but I didn't get the sense that religion was one of them. His speech in that episode had to do with his own alarm at being identified as a figure part of an older superstition which the Mintakans themselves had discarded.
I know this was several pages prior, but I just got back to this thread. Anyhoo, this is also how I saw it. I figure Picard respected various cultures and that includes the religions that formed them. He is, after all, a Frenchman, from a culture steeped in Catholicism and the Holy Church.
I think where his problem lies in "Who Watches the Watchers" is that this religion that has been cast aside as patently false is somehow being brought back to the detriment of the Mintakans, that even in the face of scientific explanation, the adherents of this religion hold fast to this nebulous lie instead of see the truth for what it is, that Picard is NOT God, that he is mortal, hence the quote of Arthur C. Clarke's "
Any sufficiently advanced technology is indistinguishable from magic". One such as Picard seems fascinated by various religions and cultures, not disdainful of them. "The Chase" has a great example of Picard's love of cultures and ancient beliefs, and our modern religions tend to fall under "Ancient Beliefs" seeing as they are a thousand to several thousand years old.
I think WWTW tries to make the case that blind acceptance of religion an denial of people and events around you, even in the face of cold hard fact, is detrimental to society and needs to be cast aside. That is how I see that episode, and as a Christian, I can say it's definitely one of my favorites.
J.