Short answer as far as i know. "witches" were burned cause they were scapegoat for anything bad that happened.
Bad harvest? Witch Curse!
Animal dieing of sickness? Witch Course!
Dead Born Baby? you know the drill by now.
also that there were old Ladys who just knew more about flowers,medicine and weather then most People did add to the whole "they are users of dark Magic" bit that most folk believed.