My experience has been overwhelmingly positive, both the 2 years I lived in Japan from 2000-02 and the 2 months I've recently again lived in Japan. Only one time did my wife and I encounter an overt racist, and the comment was directed at my wife regarding our international relationship. It was in Sasebo, a Naval base town in Kyushu, so that's understandable. It's not like typical servicemen are college educated and trained in intercultural communication and endeavor to promote harmonious international relationships. Many of them on leave just want to get drunk, act like apes, and slobber all over the local girls. To be fair though, I've witnessed non-military types walking all over Japanese because they know that they can get away with behaving in a manner that would get their asses kicked for it back home. Like the Halloween party train on the Osaka loop line and how it started out as just lighthearted fun, but when it got too big, they became disruptive towards other commuters and were very raucous and rude.
If you go out of your way to be courteous and show respect towards others (something I know many Americans are incapable of), then you will do fine. With the job in Nagano-ken I just left, I had several school faculty tell me that they were very disappointed that I was leaving because I knew the language and the culture. One even said I have "Yamato Damashii" because of my work ethic. When my mom died, I insisted on continuing to teach classes because for me, seeing the kids' smiling faces made me feel better than staying at home, crying. Everyone expected me to run off to America and leave everyone hanging, which a typical ALT would do.
I think most of the anti-foreigner crowd just sulks online on places like 2ch or YouTube to spew their venom, but most of them probably wouldn't dare to insult foreigners in person. If you'll allow me to rant a bit, I've recently encountered a rather bizarre specimen who calls himself "Novajoke" on YouTube and apparently other places. He can communicate in English effectively enough, but he hates the idea of native English speakers teaching English in Japan and calls them "parasite gaijin losers." He is so convinced that every single English teachers is identical and a threat to Japanese society. Since I am an American teaching English in Japan, he has accused me of numerous, terrible things and his assumptions are baseless and 100% inaccurate. With each absurd prejudice he reveals about me, I have refuted him every time. He has accused me of so many ridiculous things, like being a burger flipper living with my parents, a dishonest sales person, a sexual predator, a pedophile, a criminal, and anything he can imagine, just because he has read news clips about foreigners in Japan committing these things. I've known perfectly decent foreign ALT teachers who have been sexually assaulted and have had their property stolen by Japanese citizens, but it would be insane for me to categorize all Japanese citizens of being like this. However, he has no shame in accusing me of these things. Any normal person would probably feel embarrassed having made such wild, false accusations, but this guy is not just a xenophobic bigot, but a neurotic imbecile as well. Anyhow,
I summarized my exchange with this psychopath on my homepage because his insane rantings have been quite amusing.
I honestly feel sorry for the guy, but he has not only insulted me, but my wife as well. He is mentally unsound, so refuting his angry accusations is just a waste of time. I swear, this guy gets so worked up at the thought of foreigners living in his country who do not 100% agree with him and condone his belligerent, racist stereotyping, that he's probably going to have a brain aneurism one of these days. Allowing myself to get angry with someone who surrounds himself with nothing but anger is a waste of time.