Japan's rail network is the reason most itineraries here need no other mode. This page lists eight bookable journeys, and the measured times explain the shape of the country: Kyoto to Osaka in half an hour, Tokyo to Kyoto in two hours and twenty-five minutes, Tokyo to Hiroshima in four hours. Narita to central Tokyo is one hour.
The decision that costs money is the JR Pass. It covers nearly all Japan Railways services for seven, fourteen or twenty-one consecutive days, and it pays for itself across two or three intercity journeys — Tokyo, Kyoto and Hiroshima is the shape that works. If you are staying mostly in one city it is less worthwhile, because the pass is a travel ticket and not a discount.
One exclusion catches people out. Nozomi, the fastest Shinkansen service on the Tokyo–Kyoto–Osaka route, is not included with the pass. Planning a pass itinerary therefore means checking which service each departure is, not only which route it runs. Reserve seats in advance during cherry blossom and autumn foliage seasons, and check the last departure if you land late: airport train service thins out at night.