That's only part of it. Do you mean intra-city transit or inter-city transit? Highways are used by car drivers to move within the city (or between cities in the same metro area, such as between Yokohama and Tokyo), not just between far-apart metro areas.

One huge difference between the US and Japan here is parking. Having a car is one thing, but where are you going to park it when you arrive at your destination? If you're driving between two towns or smaller cities, this might not be an issue, but if you're driving between Yokohama and Tokyo, it probably is. The car is only a feasible choice if you're traveling between points where there's a place for you to park. So of course, this drives a lot of traffic onto the trains and keeps ridership very high.

Both, and both. Both intracity transit and Amtrak is a total joke, and if anything Amtrak is significantly worse, with some intercity connections not even having daily service.

This is entirely a policy choice. America subsidizes parking by requiring very high parking per place, and since they’re required to build it anyways and there is so much supply it is always free.

Japan does not subsidize parking like this, in fact quite the opposite. There is no free street parking and to buy a car you need proof of a parking spot to store it in, and parking is more of a market as a result.