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).
I feel like people forget how much infrastructure is required to keep high speed rail running. Not only do you need the stations, but the tracks (bridges, tunnels, etc.) all need to be maintained. Additionally, when doing maintenance you can’t run the line, so you either need extra capacity so you don’t disrupt service or you end up with times you have to shut lines down.
In comparison, planes just need a strip of flat land at takeoff and landing (you technically don’t even need an airport). You’re primary bottleneck is how fast you can get planes on/off the tarmac.
One of the other big issues in rail vs plane is that high speed rail only works at certain grade levels and turn radiuses. So for example, I believe you couldn’t convert the existing northeast corridor in the US to 300mph rail from end to end simply due to the geography. You’d need to create a new route. Looking it up there are speed limits around 30-40mph for Amtrak around Baltimore and Wilmington.