Kaylee liked Simon, that much was obvious. Sure Kaylee liked most people, but she liked him more than most. She was honest enough to know that part of it was his good looks but she also liked who he was inside, that sweet kind man.
She knew he wasn't use to this life and that trying to help his little sister was hard. That was why she forgave him when he said things that hurt her. Most of the time Simon was just speaking without thinking, and knew why he'd hurt her and was sorry for it. If she was honest Kaylee was never really that upset those times, though she was often angry with him.
But there were other times when he'd say something, look up, see the hurt in her eyes and not understand. Sure he knew he'd hurt her and was sorry for it but he didn't understand why what he'd said was hurtful. It was these times that really upset her, because she worried that one day Simon might do something that broke her heart and not understand why.