To be honest, that comment is objectively right in doing this. It's very easy to take a single, localized event - whether negative or positive - and start generalizing from it, reaching wrong conclusions.
Still, if one is to feel ashamed for the bad things happening within a group one associates with (e.g. their country), it's fair to also feel proud for the good things happening within that group.
I don't believe that a positive story about Japan is going to mislead anyone into thinking the place is all rainbows. I don't believe it needs to be tempered by a negative story which I believe is more damaging and unfortunately more memorable.
Still, if one is to feel ashamed for the bad things happening within a group one associates with (e.g. their country), it's fair to also feel proud for the good things happening within that group.