What does McMurphy mean when he says that the nurse isn't the root of the trouble?

The Nurse would not have as much power over the men if she did not have them in a highly controlled situation in which she is allowed to get away with her treatment of them. She simply is exhibiting a kind of behavior that is tolerated by her superiors and cannot be questioned by those under her. There is no reason for her to stop behaving this way; the root of the trouble is the way the patients and their needs are perceived.