all i can say, in generally they are really non-racist people or better said, they just gife a shit on racial things. of course there are always some rare exceptions, but where on that damn world are non of them?
some elder people may like to have some distances to foreigner, due to 2nd WW happenings. but also there, just in very very rare cases and mostly very locally concerned where those sad happenings took place. nevertheless, e.g. nagasaki is one of the most friendly places with a lot of foreigner living there.
in the other hand, a lot of em are not used of how to handle foreigners exactly do to lack of experience, so a natural reaction as a result is trying to keep some distance, rather than doing something wrong.
some people claimimg, that they didn't let them into a bar or waht ever due to "no gaijin allowed" plate etc. i heard of those existence, but have never seen one by myself. but what i heard or read off is, that there is always a story behind, of why it came that far of prevent gaijins of entering certain private properties. rarely there are any racial toughts behind.
as for me, in my 3 1/2 years, i never faced anything that just comes close to racial exclusion or such. very friendly, very welcomed! to the very contrary of how my wife was threatened in my home country sheer daily, just due to here asia look -> could fill books with stories!!
so all around, i honestly can say that japan is now one of the most pacificistic, very harmless and lesser racist oriented country in this world and the people are very polite (probably one of the most polite nations of all). they may be proud on their nationality and loving it to keep up some good old traditon, kinda patriotic oriented you may call em, but that has nothing to do of being a racist.
there are a lot things which stinks in japan thought, but i wouldn't count racism in there. and those bratts on that site you postet above are pure sensation captors fuul of hatred!!
better first watch of how things working in their own country, before shouting overdriven bullshit like that!