So the rooster is the only adult chicken in your flock now? If so, he may be taking on the job of nurturing. It happens some times. There are gentle pecks delivered to the back that aren't aggressive but disciplinary.
If he pecks on the head of a chick, that's dangerous aggression, though. The chicks need to have a place where they can run to that the rooster can't follow to continue his attacks. That's why I recommend a protective enclosure with chick-size openings.
It doesn't have to be a fixed pen, either. If you free range all of them, you can utilize a pet crate with a modified door covering with a chick-size hole cut into some hardware cloth with sharp edges taped over.
Or just pen the rooster away from the chicks until they get to be full-size.