Actually, Japan is arguably more tolerant of incest than the US.
If you mean in regards to cousins, then yes. Most places are. But in Japan, not only is there less acceptance of same-sex relationships, sexuality in general is not something you typically share. Add to that the fact that this is about a parent and child, and you get incest that is not only more taboo than sibling incest, but also something that no kid would ever feel they could ask their parent about.
In Japan, sexuality in reality and sexuality in fiction are far more drastically removed from each other than in the U.S. Keep that in mind.
That ending was so sad. Can you imagine how confusing and distressing that would be in a repressed society like Japan? I want to give her a hug and tell her everything's okay.