There are many reasons. There are quality issues, there are cultural issues, there are game library issues.
(1) Quality issues: The original Xbox was regarded as low quality -- it scratched disks, it was very large (seen as technologically inferior), etc. The 360 has really expanded on the low quality sentiment. While the 360 has been designed better aesthetically, it still has DVD drive quality issues and other hardware quality issues.
It's worth noting that Japan's population overall is very dense and they tend to have smaller living spaces than the average American. So small devices, including smaller and cooler electronics, are valued more than in the US. The Wii, DS-lite, PSP and PS2-lite really cater to Japanese in that respect.
(2) Cultural issues: it is somewhat true that the Japanese are relatively loyal to their brands. This includes a feeling that they make superior quality electronics. While is tends to be true, much of the world considers American electronics to be inferior as American electronics companies usually compete primarily on price, not on quality (there are exceptions, of course).
(3) The Japanese gamer seems much less interested in shooters and sports games, except baseball, than American gamers. These are the two strongest areas of the Xbox 360's library rendering the 360's greatest strength in the US a weakness in Japan.
While these issues are related, I think the combination thereof is really what tends to turn the country off from Microsoft. However, if you look at the PS3 vs the Xbox 360, you'll see that the PS3 isn't even doing all that much better than the Xbox 360.
Take the PS3's current sales as a baseline. Subtract the value of the Playstation brand name. Subtract the value of the Sony brand name. Add the cost of the Xbox/360 quality perception. I think that explains the performance of the Xbox 360 fairly well.









