Hispanic student in japan... will I be treated bad?

You do not need to be on guard against physical attacks, if that's what you're worried about, and you should be fine as an exchange student. Japan does have a very insular culture, but they're not hostile to outsiders. It would be very difficult for you to find work at a Japanese company, but you won't be jumped in the street or even insulted to your face. Most Japanese are very polite and don't expect foreigners to understand everything about their culture, so even if you screw up and do something that is accidentally offensive, people will be pretty tolerant. Your host family will also help you navigate the new culture. So just relax and enjoy the experience.

The Japanese people themselves have no hostile attitude towards Latinos but the immigration authority keeps discriminative policy against them. http://www.ipcdigital.com/es/Noticias/General/Enfoques/La-propuesta-del-Kono-es-una-burla-Dr-Yamaguchi Japan once loosened immigration policy to lure manual labours from sudamerica but the big economic depression sustains and they are trying to deport jobless foreigners out of Japan. Please always be sure to carry your IDs with you or you may find yourself in trouble with them. And the fact "a lot of racism" is partly right, as some of the Japanese abuses Chinese and Korean who are relative "majority of minority" and are not thought to loyal to Japan due to controversial territorial and abducting issues.