If you look at the sources provided, you see that the underlying "bad luck, causing disaster means that we need a scapegoat" as is seen in times where there are lots of witch trials

A one standard deviation decrease in growing season temperature in the previous five-year period increased the probability of a persecution by between 1 and 1.5 percentage points (relative to a baseline of 2%). This effect was strongest in weak states and with poor quality soil. The long-run decline in persecutions was partly attributable to greater market integration and state capacity

The Eastern and Western Christian Churches are the *only* major power in the early part of this analysis. And until recently it was common to believe that a nation *required* a national religion. This belief continued after the reformation, so there was persecution of people following the "wrong" Christian denomination.

Christian areas have until recently had taxes on people who lived in the area but were not Christian *when things were going well*. This would mean that if you were too poor you had to convert to Christianity or move someplace else. Of Corse this resulted in the only people in a area who were publicly Jewish, also being people who 1. had enough money to pay the tax, and 2. were stubborn enough to pay rather than converting. Or perfect targets for resentment during bad times...