Sadly, I am having this problem, too. My oldest girl is so stressed because of the dominant rooster torturing her that she no longer lays eggs, which is awful. I hate for her to be so miserable, and I have spoken to him about consequences of his actions and how he's failing at his job of protecting the flock. (Crazy, yes...I know, but I was hoping that he'd understand an check himself.) I thought he'd gotten better, but I just witnessed him go after her before lights out. Apparently jumping on the perch is a crime in his mind. Last night he went after my little White Leghorn juvenile Roo, just because he was hungry and wanted to eat. Last night's aggression got him kicked him outside into the (enclosed) chicken yard. I intended to let him stay out all night even though I felt sorry for how freaked out and unsettled he was. I would've stuck to my guns but for a horrible storm, so he got to go back inside. His antics tonight got him kicked outside for the night. I'm inside trying to figure out how to cull him in the dark, if that's any indication of how I'm feeling toward him. I don't have a greenhouse and I'm not feeling particularly inclined to build him a separate enclosure. If he's not doing his job, I don't feel any need to keep him around.
After reading the thread here, I'm thinking that culling him is my best option. I realize that chickens, like people, have their own personalities and preferences, but how he could be so mean to her is beyond me. Her back has a bald spot and so does her bum. He is just not nice to her and he doesn't deserve this great flock. I was hoping to keep him and maintain a balance with the other boy, but it seems like too high a price if my girl has to pay the toll. Off with his head.