I'm not convinced that "gods" has always meant what it means now, or that it always means an invisible entity. I think early humans had every bit the capacity for metaphor and poetic interpretation as we do now. Many of those gods represent human experiences that cannot be represented by concrete objects or straightforward activities. There's no reason to think they wouldn't have the ability or tendency to describe powerful human emotions and experiences as metaphorical entities.
What we might call a goddess today could simply be a notion representing a reverence for the miracle of motherhood. I see no reason to automatically assume fearful superstition and ignorance to every artifact and story from the ancient past. Even what we now call "ancient Greece" was a very modern time compared to, say, the time of the "Venus of Willendorf" figure. This is why some scholars would rather she be called "Woman of Willendorf." "Venus" is a much more recent concept than the time the figure was carved.
I would definitely agree that many rituals and myths were metaphoric. If you look at something like the
Trickster character that was a part of a lot of native religions, I'm not sure whether people believed that these stories were literally true.
Although, on the other hand it's not clear to me whether creation stories were believed to be literally true or not. Based on what I've read I'd lean towards that they were, but it'd be dangerous to generalise across thousands of tribes. I don't know that I'd call it fearful superstition, necessarily, just a need to explain why the hell they existed.