It is hard to know the answer. The rooster if young, may be too aggressive with her, or she may not wanting his advances. Some roosters may have a favorite, who may lose feathers and become more scraggly. Spend time with them watching behavior. Sometimes just separating the rooster until he is a bit older can help. You could keep him separate some, and let him be with them a little each day. Not every rooster is worth keeping if he harms a hen.