What were the plot conflicts in "By the Waters of Babylon" ? What did the author express by those conflicts?

To me, the main conflict in this story is between John and himself.  It is between his desire to see what is in the Place of the Gods and his fear of what will happen to him if he goes there.

I think that the author is trying to convey to us how what we think of as progress requires us to overcome fear and superstition.  John's fears are the fears of primitive people.  They are the fear of things that he does not understand.  But he overcomes those fears and will, therefore, be able to help his people progress.

However, this is not all to the good. I think the author is also telling us that we as people are doomed to keep making the same mistakes over and over -- John is going to start the human race back on the path that led to New York being destroyed.