Anatomically speaking Europeans don't look like that either. But most of the people look more European than Japanese, at least it seems to me ... Maybe it's the round eyes? And the non-black hair in some cases?
Just like Senshin stated in his comment. For the Japanese people their characters do look Asian.
There is a really nice atricle writen about this on thesocietypages And as stated there
In your question you also said "Maybe it's the round eyes? And the non-black hair in some cases?"
The society pages also pointed out something about that
"The Default Human Being thing is so strong that lacking other clear, stereotyped signs of being either black or Asian she defaults to white."*
Off course there are also exceptions a nice sample is indeed Dan Eagleman as stated by Senshin. The moment they need the feel to make somebody look non-Japanese they will try to design the user more to the american/european stereotype. Aka - Bigger noses - Blond hair/blue eyes/white - Speaks Fluent english