Japan has a majority- privatized highway network, funding it requires tolls way higher than would be politically feasible in any western country. Gas and tolls make taking the bullet train cheaper for some distances if you're alone (the equation changes if you load up your family).

I live here and have to pay the tolls but I still prefer it from a "user pays" justice POV.

It doesn't have to be privatized though - Singapore is introducing a GPS-distance-based congestion charge on their roads ("ERP 2" if you want to Google it)