Japan's railroad system has a big geographic advantage - the country is long and narrow. The railroad system is primarily a long end to end line with short crosswise branches.[1] That's an efficient structure. The branch lines don't have to be fast. Many are still narrow gauge, at 3 ft 6 in. The US had to fill a huge area in the railroad era. That left a lot of underutilized track once the road network got good. [1]…
There is no excuse for the US’s failure. Many countries have large areas to cover. China is a similar size and has massive HSR coverage. The US could too if they didn’t waste all the money on corruption.
China is also corrupt, but it is a dictatorship with massive central planning. Central planning leads to wastage and human costs in many areas but it is good at producing new infrastructure.