Frequently, the nail that sticks out sticks out because the Japanese person had the audacity to have a black or korean parent.
It has nothing to do with race; there are many similar North-West European proverbs that describe a similar tendency that advise against attempting to be exceptional.
U.S.A. society is opposite; it is known to celebrate and encourage exceptionalism and to reward those that have achieved it, or were simply born so.
And even if your interpretation were true, I see no reason why your country of residence would præclude you from criticizing something you disagree with. — the man who feels responsible for the actions of other by association, I find is is also very often the man who assigns responsibility to the innocent by association.
For the record, maybe you haven't met a nice non racist Japanese person yet, that's why your reaction is like that. There are quite a number of mixed ancestry in Japanese society, most of them do fine.