As a son and a father to a son, I understand where you are coming from. The rise of conflict between parent and child of the same sex has been part of human experience from "the beginning." The rising friction between a father and the growing son is a typical pattern in most mammals. There are hundreds of studies by anthropologists and psychologists that examine this phenomenon in great depth. Most agree that it serves a biological need to drive male offspring (who carry the same genetic "stuff") away from the "herd" or family unit to avoid excessive interbreeding. It's a matter of long term survival for a local subset of a particular species.
In humans, a father's "repulsion" of a son forces the child to develop independance. Unless your family has some major disfunctional issues, this "repulsion" is a natural process. Once the son physically leaves the family unit and is fully independent, the relationship between father and son transforms into something new - as grown up men, allies & confidantes that is based on mutual respect.