It is pretty clear that our leaders, typically looking no farther forward than the next election, have no serious plan for paying for this maintenance, not surprising since their only plan for paying for building infrastructure is gobs of debt, with no idea of how to pay it off. I very nice double inheritance for the next generation, indeed!
I would like to point out that in terms of right-of-way maintenance, rapid transit can (potentially) impose much lower future maintenance costs than highways, since the right of way is so much smaller. An overpass for two tracks has more passenger capacity than one for ten freeway lanes, but is only 20% as much bridge.
Of course, how much this matters depends on how a system is built. Most of BART in the East Bay is elevated, and that's a lot of bridge (and it is, in fact, in need of seismic upgrading). Transit systems with simpler (and cheaper) grade-level right-of-ways such as CalTrain, or (for a more modern example) the San Diego Trolley are both vastly cheaper to construct and ultimately to maintain. Of course, there are clear safety advantages to grade separation. Adding over and underpasses to transit lines gradually, where and when it will most improve safety, but not demanding it for every last industrial backstreet that happens to cross the line, is a good compromise, raising safety without imposing excessive costs--either at the time of construction or down the road.
Ideally, every infrastructure project should have a plan for paying for long-term maintenance. Fares or tolls or some sort of usage fees ideally should cover not only basic day-to-day operating expenses, but depreciation. Few, if any, are (maybe the Golden Gate Bridge?). The budget-busting rebuilding of the eastern Bay Bridge is a prime example, and BART is manouevering for bond money for seismic upgrades of the transbay tube.
Would this raise fares for transit riders? Certainly. But it would raise the cost of driving as well. As much as transit advocates like to lobby for funding, let's remember that in the long run transit really does just work better--so the more everyone has to pay the real costs of their modal choice, the better off we are.