The play, in addition to addressing sexism and gender politics, is about student-teacher power relationships and the inherent hypocrisy of the university tenure system.
John's conference with Carol in act 1 crystallizes this problem. John is distracted by the details of buying a house, which is one of several future events he anticipates as a result of gaining tenure. He does talk to Carol in a condescending and paternalistic way; his efforts to make her "understand" are filtered through his own experience as someone labeled "stupid" (which he clumsily tries to explain to Carol), and simultaneously balancing the life transition he is trying to manage over the phone while trying to talk to Carol is not helping matters.
Carol, for her part, is simply trying to dupe John; she's not really interested in his class or "understanding" his book but in documenting his sexist behavior. Even though Carol claims over and over not to understand, the play makes clear that in this situation John is the one who is unaware—both of Carol's agenda and his own unexamined motivations.
Carol's demand that his book be banned from the university and her accusation that John tried to rape her when he touched her results in John having an epiphany. John comes to see that it is only by exchanging all his intellectual principles that Carol will withdraw her report to the tenure committee and, in a rare moment of clarity, rejects this notion. Consequently, he loses his job.
Carol's insistence that "it's not for him to say" whether his touching Carol on the shoulder had sexual intent or not is another inversion of the power structure. Carol's claim that the touch was "sexual" or that his attempt to restrain her amounted to "rape" is thrown into question by the play itself: as spectators, depending on how these events are staged, we must form our own conclusions.
It's telling, however, that the one moment of clarity in John and Carol's relationship comes at the end, when he throws her to the floor in anger and towers over her with a chair.