Jonathan knows the vampire Dracula is evil, beyond a shadow of a doubt. After all, he killed Lucy, and would have taken Mina if he had had the chance. But Jonathan believed himself safe, at the beginning. Dracula seems only to feed when he intends to turn his victims, and all the evidence pointed to his taste being only for young women.
Or so Jonathan thought. He knew that Dracula had to be destroyed, for the sake of the ones he would damn for eternity by turning them, and for the sake of the ones they would kill. Jonathan knew he might die in the hunt, but he was convinced his soul was safe.
That was before the dreams started.