The trip from Tokyo to Kyoto goes through several cities that have >200k people living in them, several of them being larger than Sacramento. Your point about Tokyo -> Kyoto doesn't change the previous issue of economics of trains due to lack of density.

Stops (and Population) on Tokaido Shinkansen between Tokyo and Kyoto: Yokohama: 3mm+ Odawara: 200k+ Hamamatsu: 700k+ Shizuoka: 600k+ Nagoya: 2mm+