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 passenger 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.
Passeger 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 l> You know, I keep hearing this about road use taxes not fully paying
One book that discusses these issues is "Empire on the Hudson", which is a history of the Port Authority of NY & NJ. It discusses how they financed bridges and tunnels and went to the trouble to get tax exemption.
A history of Pennsylvania Station, NYC by William Middleton, and a history of American railroads by Don Ball both document how railroads were paying steep property taxes on their facilities. The money was used by muncipalities to build new airports, which competed with the railroads.
Another source would be your local government, to see how much they spend on public safety for streets. Each area varies in responsibility, but in general public safety services come out of your property taxes.
If a road has been widened or newly construted in your area, you could call the tax collection office and find out how much land went off the tax rolls, then ask how it will be made up.
Note that different states do things differently. In New Jersey, property taxes support a network of county roads, in Pennsylvania, the equivalent class of roads are supported by the state via gasoline taxes. Penna has higher gas taxes and lower property taxes than NJ as a result of that.
This issue of cross and indirect subsidies also applies to the telephone industry, as we've discussed here recently.