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).
That tends to be the case though. Even in Europe that’s true in many cases. I think so far only France has legislation on the books that makes it illegal for airfare to beat trainfare under a certain distance.