Arguments over transportation policy often run as follows:
HIGHWAY SUPPORTER: Highways pay for themselves! Buses/trains don't! So highways good and everything else bad bad bad!
TRANSIT SUPPORTER: But highways create bad externalities like pollution and climate change! So if highways were taxed at their true cost gas would cost a zillion billion cajillion dollars per gallon! (followed by numerous counterarguments and counter-counterarguments that I won't bore you with, except as written below...)
It seems to me that these arguments miss one point: even if the highway system as a whole pays for itself, the system is so chock full of cross-subsidies that each individual road doesn't (except for toll roads).