It is partially but not exclusively paid for by property taxes. It's actually a fairly small share of funding in some cases. The BATIC institute gives the numbers 5% and 1% for highways and transit funding respectively [1]. Moreover, funding is not evenly distributed here. Suburbs tend to have massive road networks and long commutes, but comparatively low property taxes. This creates a shortfall that generally gets made by with sales taxes and general funds.

[1] http://www.financingtransportation.org/funding_financing/fun...