Highways (and airways) require a general subsidy too, but it is unknown because it is indirect and buried in other accounts:
Highways and airports take up enormous amounts of land. Land is taxable, but when a highway or airport grows, that land is taken off the tax base. That's quite a nice subsidy. When transit was provided by private companies, they had to pay very high property taxes where their competition paid nothing.
Highways require extensive public safety services -- police, fire, rescue -- that is generally paid by local residents, not the users of the highway. On serious accidents, quite a few public safety responders and their equipment are tied up assisting in cleanup and rescue.
Highways and airports were built with tax free safe bonds which accordingly paid low interest. Transit systems were built with private bonds that had to pay a much higher interest rate. The Fed picked up the difference since the bonds were income-tax free. Note that to this day many psgr rail facilities are still on private land that is taxed.
Until about a few decades ago, private passenger trains were tightly regulated and forced by the government to run unnecessary services or charge fares too low to cover expenses. This hurt the system. When such systems became public there was substantial rebuilding necesary.
Passenger train carriers have been hit hard with modern day requirements, such as PCB and asbestos abatement of their inherited infrastructure and handicapped accessibility reconstruction. All of that is very expensive.
As are highways. The Big Dig in Boston cost $25 billion.
Transit lines have the advantage of being about to snake around things and be underground, something impractical for most highways.