I've often wondered along similar lines, and my explanation was always related to what's mentioned in the article as well: the Black Death killed around two thirds of the European population, without rats being identified as the main source of the disease. So today's Europeans (and Americans with European ancestry) have a high probability of being ancestors of people who, for whatever odd reason, had an intrinsic aversion to rats.
This doesn't affect your evolutionary argument, but rats didn't spread the Black Death. Human lice was the carrier. We've only recently confirmed this previously minority theory through genetic evidence, but it always fit the data better. Goes to show that there is some sort of deeply held aversion to rats such that people were more willing to believe that explanation.
I don't understand it. I think mice and rats are cute :\
I learned about it on a BBC documentary about the Black Death I saw a few years back. I'm about to run out the door so I haven't the time to properly figure out which one and see what paper they were citing. But I remember it was a French university that did the genetic tests, IIRC.
The data which fit that theory better came from London and some city in Scotland (Glasgow? I'm not sure.) Basically there were houses which shared gardens (where rats would live) but the disease didn't spread between the two houses. Likewise in London there was a poor district that got hit hard, and a rich district next door that saw very few infections. Due to the way the sewers were laid out, the rat population was the same between the two. But the lice wouldn't have transferred without close contact, which of course rarely happened between rich and poor.
The more damning evidence was out of Scotland where the doctor making a very detailed study showed that the disease only transferred between people who shared close living quarters. And in particular, during a lockdown with all-day curfew it didn't transmit at all. But where beds were reused, the new inhabitants got sick.
But the genetic evidence sealed the deal. I'll have to look up that French study later.
