I don't pick up my rooster, or cuddle with him, but most of the time he is a very good rooster. He does a good job and is not rough with the girls. He does, however, want to protect them if I have to pick one up for any purpose. He will come running and dance a little jig in a threatening posture. Not out of meanness, you understand, but I still don't let him do this.
The first time, he pecked me when I reached up beside him to remove a gal from the roost. I cuffed him lightly but firmly around the head. The next time I reached for a hen, he turned his head to the opposite side and tucked it under his wing! Smart boy!
The second time, I was removing a broody from the nest and she was making a racket something fierce! He came running into the coop and started doing his little dance towards me. I picked up a stick I keep handy and lit his little butt up! He was hopping around trying to get away and out the door!
Now, if I have an episode like this and he comes running, I just turn towards him, face him down and say, "You sure you want to do that?" He just politely leaves the coop and mouths off a lot.....
outside!
Gotta show 'em whose boss and the smart ones will learn. If they aren't smart enough to learn, do you want that bloodline bred back into your flock?