Immigration policies aside the only time I was told "sorry, Japanes only" was in Kabukicho. I think you can guess what sort of establishment that was.
I think the Japanese are a bit overly protective of their culture because they can see that Japanese society works as society is supposed to.
They can also see that other societies don't work that way and they don't want to lose that.
Otherwise they are the most courteous and friendly (and shy) people I've ever encountered.
Maybe you were not at the huge Tower Records in Tokyo back in the 90's when they had a sign in Japanese saying:
"Sorry about the theft detection systems employed, but we usually have a lot of foreigners in the store."
Maybe you were never married to a Japanese woman, you'll see how friendly they get when you try to really mix with them, not just tourist around...
Maybe you were not born outside of Japan having Japanese blood, where they treat them like outcasts... just for that...
Oh, and you should ride the J R during Friday's night, you'll see how civilized they are, puking around the train and lifting woman's skirts drunk...
Moreover, they treat their women like objects, so disrespectful towards females...
All that is so ironic, when the stereotype of the Japanese is an extremely respectful guy, that is really shocking when you really mix with them, you'll discover a lot of issues there.