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).
This doesn’t answer anything about what’s stopping America from having both.
You are taking about half empty trains in a country that’s suffering from population decline. Japan’s airlines are struggling to fill sets and make profits dispite benefiting from government subsidies that the main companies that run Shinkansen don’t get.