Never played Fallout. Shameful I know.
As for the religious imagery. There is a distinct difference between referencing religions and myths and their iconography versus having a religious agenda (Which I don't think he had, maybe I need to watch it again tho).
That said, I'm atheist as well. But growing up in a Catholic family affects who I am today. My head is full of iconography, songs, stories, prayers, guilt. All coming from my religious upbringing, and no number of issues of Skeptic Magazine is going to exorcise that from me. I expect many other people are like this. For some people this stuff just bubbles up to the surface and comes out in the form of crazy fucking art. Or a post office shooting. Y'know which ever comes first.