You gotta be kidding to ask why the learning didn’t protect up from the holocaust. I’m sure you know the state of Yiddishkeit then. Most Freye today are Frey from that time.
The same goes for Spain. You can read the Sefarim from that time to see what they say about the reasons for that Gezeira.
Another thing to keep in mind is, just as you wouldn’t laugh at eating healthy after finding out about a health nut who became sick, so too, when Hashem tells us how he runs the world, don’t scoff at Him based on a certain example.