When we want to ask the reason for something, we can simply ask Why are you leaving? for example.
But we can also ask the more elaborate Why is it that you are leaving?
On the face of it there is no difference: both are asking for an reason. But the form with is it that is more specifically asking for an explanation, and often suggests that we have some emotion attached to it: annoyance, or surprise, or disbelief.
So your example is the embedded form of Why is it that ritual gave birth to the windmill? again asking for an explanation rather than any other kind of expression of a reason.
We can see why it is that ritual gave birth to the windmill therefore means something like We can grasp an explanation of how it happened that ritual gave birth to the windmill. This is a bit more specific than we can see why ritual gave birth to the windmill, though the difference is slight.
I think Peter Jennings is right that there is also an ambiguity in whether that is demonstrative ("that (particular) ritual") or a subordinator; but actually this is not relevant for your question.