Blonde isn't a natural Japanese hair color, so the only people with it have bleached it intentionally. The most common people to do so are teenage/young adult delinquents trying to standout, who were very much unliked by basically everyone for a lot of reasons. It ranged from begrudging tolerance to outright stigmatization.

While they have somewhat relaxed their views on it to not assume the person it an outright criminal for having it, similar to how the West softened on tattoos/piercings/hair dye ourselves, it still has a stereotype associated with it. Enough so that modern Japanese media uses it as a shorthand for standard character types quite often, even in universes with all sorts of hair colors also present.

These are very collectivist, social cohesion people. It being associated with punks and other hoodlums isn't nearly as easy for them to brushoff as it is for us.