I have been to Japan and have never felt as if I was being discriminated against for any ill reasons. I found it quite nice to see a more closed society wanting only their serene ways. I speak Japanese pretty well and had no problems. It is not a racial or country-specific thing; it would be wrong if it were.
I got into places that didn't allow gaijin simply because I spoke the language and didn't make a huge fuss if turned away at first. I was about to enter a restaurant and didn't see the sign. The man told me to leave and I politely apologized in Japanese, bowed and went to leave. The man said in Japanese that it was all right to come in if I spoke Japanese and promised not to make a ruckus. I had a really nice dinner with some lovely music.
The problem is ignorant foreign people not understanding the language and ways. I'm sure that if someone here in the United States who only spoke Japanese made a fuss because he couldn't order coffee from a shop and then yelled in Japanese that we were discriminating against him, we would have similar policies.