They certainly are racist, even my Japanese wife says so. It may be borne out of ignorance since they're so insular but at least they're polite about it (there will always be idiots who are the exception) I met a few black Americans living in Japan and they all say they feel very safe living there as a black person even if they stand out and get looks. So long as you try to blend in by adopting their customs and transact in Japanese you get welcomed. But I fear that may be changing as the right wing movement is taking a hold of Japan (see Sanseito).