[cjsplat]

The airlines frequently have extreme discounts on tourist flights - similar to rail passes you need to buy these before you arrive in Japan.

As everyone has mentioned, the trains in Japan are wonderful, but if you get a tourist rail pass you might consider taking a long flight for your first leg (eg. Haneda to Hokkaido or Kyushu), then firing up the rail pass when you finish there and meander your way back on the train.

As a footnote, the rail pass is also good for a large number of bus lines, ferries, etc, so don't assume that you will have to stay in city centers.