That is one of the best episodes of Star Trek ever, an I really love the message. TOS had good episodes about Kirk taking down various gods too. Roddenberry created various god-like beings (such as Q), but note how revering or obeying these things is never portrayed as a good thing.No, he did not. TNG Who Watches the Watchers is the thesis of his religious beliefs, which is to say, he had none and considered religions superstitious nonsense that held civilizations back.
I really find it perplexing that a person who likes 'Gene's Vision' (and I do too, regardless his failings in his personal life) would see his atheism as a bad thing. It informed his vision and how it influenced the franchise is one of the best things Roddenberry brought into Star Trek.