Like any place you're planning to move to, you'll want to do a lot of research ahead of time, particularly if your looking for a place to rent or live. While the language barrier makes things a bit more difficult, I don't believe Japan is any different than most places. I would say that article is spreading a whole heap of fear, uncertainty and doubt.
I found Japan to be very accommodating and friendly. In cases where the language barrier was an issue, a Japanese person may feel overly embarrassed so they may not feel comfortable helping, but I would certainly not say that Japanese people are entrenched with discrimination toward foreigners. That's just plain silly.
KingDog san, Konnichiwa. Thank you for posting your thoughts.
insidious.environment san, konnichiwa. I think good people are everywhere vice versa. Although the articles must have been written based on facts, I believe many people have good stories in Japan, too.
insidious.environment san, konnichiwa. I can understand you are worried about new place where you haven’t been. I had lived in other countries and worked there and met both good people and unkind people. If you keep in mind the proverb, “when in Rome, do as the Romans do”, and try to be polite, you can live in Japan. Gannbatte kudasai. I cheer you.
You should bear in mind that the sort of people that write articles like this are the same people that would turn around and accuse Western cultures of "white privilege" over things like band-aid colors or asking where someone is from.
I was actually worried about it at one point, and it stopped me from learning Japanese for several years. The widely-held idea that no one in Japan was capable of befriending a foreigner unless they were getting something out of it was quite a turn-off. When I went to learn Japanese in a class, I was surrounded by all these anime/manga nerds that had no intention of ever using their Japanese with actual Japanese people, due to their acceptance of this fact. I didn't really like the attitudes of my classmates, so I dropped the class and decided not to learn the language.
Two things changed my mind, however. First, I've noticed that every single minority community ever has the exact same attitudes about the United States and Europe that the writers of that article have about Japan. I analyzed it all very carefully, and I've come to the conclusion that people who say things like this about any remotely civilized society are usually speaking from deep-seated insecurities and paranoia. While I'm sure there are many xenophobic people in Japan, that could be said of any country in the world. When you're in a foreign land, you tend to feel strange being surrounded by people who look different from you... everything they direct at you could make you feel uncomfortable, you feel awkward about the language and cultural gap, and you might project your own feelings of not belonging onto them. And from there, it only takes an encounter or two with a genuinely xenophobic person to color your whole perception.
The second thing is that most people don't have many friends outside their own family, even in the US. Most human beings in general really don't care about you unless you're related to them, or you can do something for them. That's a problem with humanity rather than Japanese culture. I have a ton of Facebook friends, but they never talk to me unless they want me to be a character reference or something. Sure, sometimes you can pin people down into spending time with you by doing things for them and making them feel obligated to you, but that's not much of a friendship if you're doing all the work to make someone want to spend time with you.
Not that different from how I was always stuck doing the entire group's work for group projects in school because everyone else was lazy, and they knew they could take advantage of my unwillingness to wait until the last minute and concern about the success of the project to make me do all the work. They were all really friendly until the project was done, and then after that they essentially didn't know me. The truth is, after graduating from University, most people are too worried about taking care of their family to have much time for friends... dealing with relatives and co-workers is more than enough obligation already.
The biggest exception, in any culture, would be people who congregate because they have a common interest. Maybe you like hiking, sports, computers, etc... and surely if you can find people that share your interests in Japan, some of them would associate with you. People do tend to like being around those who are like themselves, and that doesn't necessarily mean race or culture. But the problem is that most people aren't really passionate about anything besides their family or their job, so they tend to have very limited circles of people outside of family, co-workers, and maybe a few school friends.
In summary, there's nothing wrong with Japanese people that isn't wrong with overworked and isolated modern man in general.