iPhone is popular in Japan, but the market works against it:
It's carried by Softbank, the #3 player in the market after Docomo and au. Softbank's market share means that the #1-selling phone on the Softbank network for any particular month is around #25 among all phones in Japan.
For most new phones, the peak sales period is the first 6 weeks after release. After that, the numbers plummet. In contrast, iPhone has been Softbank's best-selling phone month after month. The only product I've identified with a similar sales profile is Softbank's 815T, a Toshiba product with replaceable covers that has been selling in reasonable numbers for around a year. Therefore, in terms of the market available to it (i.e. Softbank subscribers), the iPhone is a very successful product.
It does miss many features Japanese take for granted, such as 1seg, but it succeeds despite that. In Japan, form over function can win through.