The US doesn't have effective passenger rail systems for the same reason that Europe and Japan don't have effective freight rail systems: you have to optimize for one use case or the other or else have two completely separate systems, which takes up a lot of extra land.
There is also another reason, which is that passenger rail makes sense only in specific geographic and economic circumstances, and outside of Northeastern corridor, these are very few. Commuter rail requires urban population densities that do not exist in most US metros. Intercity passenger rail only makes sense at a very limited scope until air travel beats it on both speed and cost. Europe and Asia just have different patterns of development.
>for the same reason that Europe and Japan don't have effective freight rail systems
...don't we? I'm not sure about the effectiveness or how to measure it, but I know that a lot of cargo - especially long distance cargo - travels by rail.
Europe has, by proportion, significantly more trucking and significantly less rail freight than the United States. Relatedly, the average American freight train is 2-3x longer than the maximum allowed length of a European freight train.
