Each flock has its own dynamics and each chicken has its own personality, but what you are describing is pretty normal.
At 12 weeks, they may not even recognize him as male but are just doing the normal pick on an immature chicken thing. More mature chickens outrank less mature chickens in the pecking order and tend to reinforce that position like you describe.
But it is extremely common for older hens to pick on a younger rooster. They can really be brutes about it. Older hens expect a rooster to find them nice food, dance before trying to mate, watch for predators, break up fights, and keep peace in the flock. Young roosters don't know how to do that, so the older hens do not respect him at all. Besides, he needs to mature enough to WOW them with his brilliant and magnificent personality for them to obey him. It's not just a matter of size but much more of personality.
I've had a 15 week old rooster that the older hens accepted. That is extremely rare. I currently have an 8 month old that the younger hens accept but the older hens regularly kick his butt. I guess it is easier to impress young girls than a mature hen that can see beyond his surface beauty.
I can't tell you when the hens will accept him for mating and as the flockmaster. Probably still several months away. Once they get used to his presence, they may tolerate him and quit chasing him unless he invades their personal space or starts to mess with them. He'll probably hang on the outskirts of the flock for quite some time yet.
There is nothing unusual or cruel in what you are seeing. It's just chickens being chickens.
