That is almost entirely due to issues with politics and public policy. The actual physical construction of the rails would easily be the most simple part of the process. As you pointed out, maintenance would have costs, but it's not like existing rails don't include similar costs as well. Certainly there are many parts of the US where those costs would be lower than the equivalent in Japan anyway, since their climate is generally more temperamental than say, almost anywhere along the US West Coast.
It was a choice in the US to build the free-to-use interstate system just as it was a choice in Japan to build the shinkansen. The highway system in Japan is not free; it is tolled and it costs roughly the same in tolls for a single person to drive vs use the shinkansen. Local trains in most cities are good too. With these policies, applied over decades, trains became the default mode of transportation.
Also, Japan is very mountainous making it probably one of the most expensive countries To build rail in. But it’s a moot point because they managed to build up a national highway system as well as a it national train system, I think proving that it’s a matter of policy and not geography.
The other common argument is difference in population density, but this also misses the mark for 2 reasons. First of all, the US had a pretty impressive network of rail before it has an impressive highway system, it’s just mostly used for freight now and policy for public transportation shifted to roads. Second, at least the 2 coasts have high population density more or less covered by a straight line which ought to be well served by fast trains.
Because the geography of the US is quite different from Japan. In Japan you follow the coasts to reach each city: it's a straight line to simplify things. In the US you would need a lot more tracks to cover the territory, and tracks are super expensive to build and maintain.