The Jews were getting killed, and not only by the plague. Even though only 20% of the population died because of the plague, many were accused and burnt.
The Jews were very clean and sanitary, taking showers almost every week and washing there hands before praying to God (everyday). This resulted in less deaths from the plague, but gave the Christians more reason to blame.
The Muslims, like the Jews, were very sanitary. There were public bathes and every week, and it was required to bathe oneself. The dead/sick were put in separate, but clean areas and burned (dead).
Even though the Muslims weren't blamed and burnt, they were persecuted for a different reason.