Doesn't help she was married to a Vampire. A person with dark magical powers who took in all those who shunned God or were shunned by the light.
He only really married again because Lisa reminded him so much of Elizabetha. She was the only light in his life, and while he shared his dark knowledge with those that came to him, he had no particular contempt towards humans, although they might have had contempt for him. Or at least feared him. Since she was a Healer (Women "doctors"? in the 1400's? I don't think so.), something already shrouded in mysticism, they pretty much came to the only obvious conclusion- that she was a heretic and a witch, married to some dark sorceror king, and burned her at the stake.
Also, interesting note, that the year CV3 takes place is the same supposed year of Vlad Dracula's irl death.
Meaning, Vlad the Impaler's historical assassins were Trevor Belmont and his crew. XD