Service performance. Train ride in Japan is comfortable, fast, and on-time. (Highway in Japan has quite low speed limit that standard intercity train is faster on many routes)
Japanese train is quite expensive, but people feels that it's worth the money. Couple that with the fact that Japanese Taiheiyo belt is among the biggest, most densely populated area in the world, you can see where this is coming. At least 10 trains (14 on peak hour) of ~1300-seat, 400-meter-long Shinkansen trains depart Tokyo station for Nagoya/Osaka every hour from 6.00~24.00. It's even more frequent than subway service in many cities.
The fun thing about rail service is that maintenance cost does not go up very much with more train. So Shinkansen (especially the Tokaido Shinkansen) bring in a LOT of money, enough for the operating company (JR Central) to invest in building the new maglev Chuo Shinkansen all by itself.
Of course, local train lines outside major cities in in Japan are also struggling.