I really don't think it's fair to simplify this story as "religion is superstitious nonsense." It's not possible to be a person of faith and not acknowledge that the spiritual dimension of the universe does not intercede at every possible juncture. The fact that there was no intercession at this point of the story does not make the story anti-religion. In fact, that one of the characters was intensely spiritual, of not quite sure how he fit into the faith of his people, in my mind gives this story a very balanced perspective.
In my mind, this story was about a setting encountering one of the beginnings of modernity: the introduction of choice into the matter of religion. For most of ancient history, people didn't get to chose. You had the religion of your parents, or the religion that was forced on you by the victorious invaders. Then modernity - with its ideas about rights and consciences and freedoms - showed up, and people started to imagine that they could pick. Of course, if the question is "which religion?" the question can also easily by "why religion at all?" This story applied that cultural transformation - and the birth of the Anglican Church - as its jumping-off point to ask that question of a fantasy world.
I'm happy to say that this is NOT one of those posts where I find myself intellectually defending a story I didn't like. I loved this one. I really enjoy applying an intellectual approach of culture, politics, religion, and economics to fantasy settings. I enjoy how the settings mutate under the pressure, and the stories that result. This tale was, in my opinion, an examplar of the subgenre, with excellent characters and a nifty (if, perhaps, not inspired) setting.
I suppose the setting was a little generic. That's probably what the author was going for - fewer details to distract from the plot and theme - but I enjoy those details, and that choice rarely satisfies me. That said, it was still an excellent story and a pleasure to listen to.