You should separate the broody and her clutch from the rest of the flock. It’s not just the rooster that will bully and possibly kill the chicks, but the hens will be equally as nasty (most of the time - it’s best not to take chances). When you separate her, leave chick food and fresh water in there for her - she doesn’t need layer feed or extra calcium as she’s not laying and the extra protein in the chick food will be very good for her. All you have to do is provide shelter from the rest of the flock, chick food and fresh water. Mama hen will do the rest.
She is separated in her own coop but I have no clue where to put my rooster because he is very aggressive with other hens and is only gentle with my broody hen
That’s definitely a problem; he shouldn’t be aggressive towards any of your hens at all.... can you separate him for a couple of days, from everybody and see if that knocks him down a notch or two? The broody should really be alone so no one messes with the chicks... he may still not react very well to the chicks, it’s one of those things you have to keep an eye on
