Highway funding for one. Instead of improving highway infrastructure with tax money, improve rail lines.

Indeed. Trucks cause several orders of magnitude more road wear than cars, because road wear scales like weight per wheel to the fourth power (this might not always be the perfect model http://www.nvfnorden.org/lisalib/getfile.aspx?itemid=261 but even so the general idea holds), and trucks weigh a whole lot. If trucks had to pay their fair share of road maintenance, shipping by truck would probably be noticeably more expensive.

Federal highway funding appears to be mostly funded by gas taxes on highway users. It costs $44B, and $39B is funded by gas tax revenue.

While $5B is still a lot of money, it's smaller than the $8B that funds mass transit.

Trucks do disproportionately more damage do the roads than they pay in taxes for fuel, though. You're subsidizing trucking every time you fuel up your passenger vehicle.

This is the reason, at the federal level, diesel fuel is taxed more than gasoline. Diesel = 24.4c/gal and Gas = 18.4c/gal.

The difference isn't enough to compensate for the increased wear but there is a difference.

Are you sure? Truck burns 6 miles/ gallon. New EPA regulations in 21 century actually increased fuel consumptions since about 20% of engine's power goes to cleaning the air. Modern car use 30+Miles/gallon.

Road wear isn't linear with weight. Estimates I've seen put a heavy 18-wheeler at the equivalent of more than 9,000 cars traveling over the same stretch of road. Way, way more than 5x the damage (6mpg vs 30mpg).

This subsidy is going to take an interesting turn with vehicle electrification. Right now the lower the MPG, the more taxes you pay. Moving to a tax per miles driven is going to punish those that have the most efficient vehicles in a more upfront manner than it is today (Hidden in gasoline prices).