Hoyt knows Isabelle didn't like him. He just didn't know how much.
He knows every time he berates Thomas or says something about his face, Isabelle glares at him. Whenever he doesn't let her see Thomas, she gives him such an acid glare that he could feel it. It got worse after he killed the sheriff and told Thomas to start killing people. She looks at him with such hatred that he nearly flinches.
One time, he yelled at Thomas for losing someone in the basement (who Hoyt caught and killed) and he called him a retard. The next morning, the tires of his squad car were slashed.
Then Isabelle appeared and when she walked by Hoyt, she gave him a small smirk. Hoyt stared at her in shock, a cold knot forming in his gut.
He knows what Thomas is capable of, but Isabelle was another story. He had no idea what she was capable of.
He has no idea what she could do with that hate.
AN: I don't like Hoyt, when he became Hoyt. He became meaner and more of a douche towards Thomas. So, I put Isabelle doesn't like him either and she does stuff when he's mean to Thomas. I put that Hoyt is scared of her because she usually calm and the calm ones are usually the most violent ones. Yup, you better be scared of her, Hoyt!