The U.S had the greatest rail network and then we built the Interstate Highway system and abandoned rail. Truth is that nobody funds multiple competing transportation network. Japan chose rail, we chose highways.
Highways are great when everyone has a different path.
Japan has most (but not all) of its large destinations on the pacific coast, which works great for rail.
I'm sure passenger rail networks used to have more routing options than amtrak does now, but it's hard to get between a lot of places by rail without going through Chicago. In the western US, you can go north/south in the pacific states or near the missisipi. Sure mountains are hard to cross, but there's no north/south in the plains either... Or Atlanta to Florida, etc.