The Shinkansen is expensive; with the rise of low-cost carriers, any train trip that takes more than two hours from Tokyo is less cost-effective than flying.
Nonsense. Narita airport is about an hour away from central Tokyo (by one of two express trains, probably longer by car), and Haneda about 30-40 minutes (by monorail, probably longer by car). Then you get to deal with being in an airport. Both run more smoothly than the ones in the US, but still require early arrival for boarding. Flights are _far_ more likely to have delays. Then you get to deal with another airport again after landing, especially if you checked luggage.
Contrast with the shinkansen: trains leave every 10-15 minutes from the center of the city, have better seats (and green or first-class costs a fraction of a first-class plane ticket), and no dealing with airport security or lines at all.
It would take a 4-5 hour trip minimum for me to fly rather than take a train in Japan.