The onset of the Cold War was the principle driver of the divergence of the rail industries of the Europe and Japan to the US. Before that, the US had a comparative railroad infrastructure. The reason is *not based on population density or inefficient gov't as most common assumptions would lead us to believe. In fact, it was by design. The neglect of railroads and focus on a national highway system and national aeronautics industry (airlines) was done with intention by the US gov't.
Looking at the social causes of train development without the context of geographic location is missing an important link. You have to consider the physical placement of North America to that Europe and Japan. Without its consideration, we get nagging questions like why the Northeast-Midwest US which has similar population densities to Europe (ie. France to Germany) and yet lack similar rail transit infrastructures.
The answer is rooted in the advent of atomic technology. The other facet is the physical structure of the rail itself. A system requiring such high coordination would never survive a nuclear attack. Control centers might be damaged or removed from communication channels, leaving trains without systematic direction. Let's take 1 scenario: 2 trains coming in opposite directions towards each other on the same track. Assuming they don't crash into each other, the 2 train crews would have to decide/figure out which train's itinerary is more important. Then the other train would have to back up to the next switch. It's very inefficient. Roads or airspace have no such limitations. Two cars or planes can simply navigate around each other to avoid collision; there's no fixed track. This is the reason the US used it's eminent domain credit for highway and airport projects for the greater good.
So, how does this differ for our European counterparts. The answer is the Atlantic Ocean (the same separator from the last 2 World Wars). While the nations of France and Germany are under direct threat from the massive tank columns of the Soviet Union, the communist country has no surface fleet to transport these armored vehicles to American shores. It's all bombings for the US. Given that there's a realistic 50/50 chance of 1 side winning, the European gov'ts don't have the same precautions to continue administration of their nations as their lands may be under the occupation of Soviet armies. Roads & rails get captured and used by unfriendly forces just the same. In fact, captured rails are easier to sabatoge as the French Resistance did against the Nazis.
For the US, the surviving gov'ts maintain control; so they have to decide if they want a somewhat functioning highway system or a disfunctional rail system. The situation with Japan is it's topography. As a mostly mountainous nation, the urban areas are more condensed than the flatter lands of the US. A nuclear attack on Japan would damage both rails and roads with higher probability. For the US, if roads are spread far out enough, there's a better chance of them surviving.
OT: Rails are largely regional, even in Europe and Japan. So, long distances win out to airlines, irrespective to high-speed trains. The example of the NY to LA flight is tempered by the Madrid to Stockholm counterpoint. It would equally be a long train ride. A better example may be a NYC to Buffalo, NY flight to a potential high-speed Acela train route.