The only reason it's looked down upon now is because it's bad for the gene pool, and also because it's seen as an "antiquated" practice.
No, it's also because such relationships are troublesome from a psychological perspective. A parent becoming a sexual partner changes the dynamic of a relationship in ways that cannot be undone. And let's be realistic, a father interested in having sex with his son is not going to wait until he is an adult to (a) begin fantasizing about it or (b) to begin acting on it. How would you feel if you learned your dad was only spending time with you because he thought you'd be a good fuck?
Heterosexual men who dream of these kinds of scenarios are just as disgusting. They do not get a pass either.