The roosters should go in the coop with the pullets. If they're shut out in the run, they can't take care of their ladies. But, if they are aggressive to the girls, that's a different story. Sometimes, when cockrels "come of age" they want to do nothing but breed, and breed some more. They can be brutal to the pullets who don't mature as quickly as they do, often ganging up on one pullet, usually the one at the bottom of the pecking order and brutalizing her.
