That is part of the mating ritual. When it goes as it should, the rooster dances and the hen squats. This gets her body on the ground so the rooster's weight is spread out. If she tries to stand up when the rooster is on her back, she could get hurt. The rooster hops on and grabs the back of her head. This head grab is her signal to raise her tail out of the way. The rooster quickly touches her vent with his, and he hops off. The hen stands up, fluffs up her feathers, and shakes. This fluffy shake is not her way of telling him "I've had better, Big Boy". The shake gets the sperm in the right position in her body.
It does not always go as it should and that is usually not a problem. If the hen runs away instead of squatting, sometimes the rooster walks off and forgets about it. Sometimes he chases her. As long as she squats when he catches her, if he catches her, its OK. If she resists too much, then she might get hurt. So the hen has some responsibilities to act right. But some roosters are brutes. No other way to say it. They can hurt a hen even if she does not resist. He is usually bigger than she is. They both need to do their part.
Usually the problems, if there are any, are when the rooster and/or hens are adolescents. They need to mature into their roles. If they can get through that adolescent period, things usually sort themselves out. A lot don't have those adolescent problems to start with. Some never get over them, but a majority do.
You might see some different variations of this mating ritual, but maybe you are better prepared. Good luck!!! Hope it goes well.