I'm no historian, but I read some books. My take:
1) Banking. The Old Testament bans the charging of interest, but medieval Europe found a loophole. They all decided it was OK to pay/charge interest between Christians and Jewish folks. Ie King Thomas can't loan money to King Michael, but he CAN loan it to a Jewish intermediary, who then loans it to King Michael. Presumably that's how banking ended up with lotsa Jewish people. We all hate bankers, and lotsa bankers were Jewish. So...
2) The Black Death. I guess the Old Testament has some specific rules of cleanliness. Sweep up stored grain, pick up your trash, etc. Christians fell away from that over time. Then the plague rats come in. Jewish households are unappealing and they move on, leaving their residents unharmed. Said plague rats set up shop in the homes of dirty Christians, they all get plague, they die. Christian survivors can't help but notice their Jewish friends aren't dying. They jump to the wrong conclusion...