This is an interesting article, to be sure. I am especially interested in the assertion that the human brain is primed to attribute intelligence (in the form of an unseen agent) to events which it cannot explain. Why shouldn't this propensity evolved simply as part of some self-defense mechanism?
After all, if you don't know how something that is potentially dangerous, such as lightning, works, isn't it safer to exaggerate its capacities rather than to underestimate them? By attributing lightning with a supernatural intelligence, we are better able to pump up our fight-or-flight mechanism, and the resulting fear associated with lightning will keep us safer in the long run.
You see this all the time with other irrational subjects. Take extraterrestrials, for example. Why do humans always seem to assume that if there is life on any other planets, that life would probably be intellectually superior and more technologically advanced than we are, and that it would probably be a threat to our entire existence? Isn't it more rational to assume that if there aren't any flying saucers landing here to take over the world at this point, then any life on other planets must either be at or below our own intelligence level or too far away to reach us? Why must all life on other planets be assumed to be intelligent? Is it simply because imagine life on other planets as slow-moving extraterrestrial fungi is more interesting? Or could there be some survival instinct involved in this?
If you think about it enough, you realize that attributing lightning with supernatural powers certainly functioned on some level as a survival instinct. I imagine that primitive humans who were actually frightened of the terrifying powers of the lightning god were probably a lot less likely to get struck down by a lightning bolt than those who had no fear of lightning at all.
Unfortunately, the instinct to attribute supernatural causes to unexplained phenomena doesn't work quite as well as actually researching and understanding the real causes. But given that even in the modern world, fear is a tremendous motivator, you can see how this propensity might still persist. Just as a fear of heights contains both rational and irrational elements, so to does a fear in an angry god.