Short answer: cities are too far apart and the USA is large. However, how much funding is there to really implement the same thing that exists in Japan but in the United States? Also, is there an incentive for that in the first place? What about population density? Japan is more compact regarding their population density while that’s not the case for America plus both Osaka & Kyoto aren’t too far from each other (but Miami & Washington DC are distant).
There are various issues, but one is urban design. If you get there, how do you get around? … Most major US cities are built for cars. So then airplanes make sense for long distances, but cars are better for medium range, for most people, for most destinations, on average.