Well going back to medieval Europe it's a purely religious thing: in the Bible the Jews condemned Christ, and after his death the Jewish people continued to refuse to recognize him as the Son of God. I mean that's the official line, from a more critical perspective their faith, as well as their wealth (because they were not bound by the Christian tenant against usury so some were rich money-lenders) made them into convenient scapegoats who could be blamed for all sorts of social ills, epidemics, etc.