Capacity. Rail is pretty much unbeatable in terms of pure people per hour. The Tokaido Shinkansen carried 143M people in 2012; the busiest air route in the world, Seoul-Jeju, carried 11 million people in 2015.
From the (admittedly not great) source of CAHSR:
> Providing the equivalent new capacity on the state’s highways and airports would cost more than double
the investment required to develop a high-speed rail system between San Francisco and Los Angeles. If it
was even possible, that would mean building 4,300 new highway lane miles, 115 additional airport gates,
and four new airport runways at an estimated cost of $158 billion. [...] Caltrans estimates operations and maintenance costs on those new highway lanes at
$132.8 billion for over 50 years.
Planes are terribly polluting, and unlike trains, there's no expectation that can be changed anytime soon. If you properly accounted for that externality, trains might be profitable after all.
From the (admittedly not great) source of CAHSR:
> Providing the equivalent new capacity on the state’s highways and airports would cost more than double the investment required to develop a high-speed rail system between San Francisco and Los Angeles. If it was even possible, that would mean building 4,300 new highway lane miles, 115 additional airport gates, and four new airport runways at an estimated cost of $158 billion. [...] Caltrans estimates operations and maintenance costs on those new highway lanes at $132.8 billion for over 50 years.