Fortuitously enough, just this morning, the US Public Interest Research Group (USPIRG) came out with a report on that very subject. It concludes, "Highways do not – and, except for brief periods in our nation’s history, never have – paid for themselves through the taxes that highway advocates label 'user fees.'"
Before jumping into the numbers, the report first dispenses with the idea that gas taxes are "user fees." Unlike tolls---which drivers pay to use specific roads---"the amount of money a particular driver pays in gasoline taxes bears little relationship to his or her use of roads funded by gas taxes." In fact, people pay gas taxes for the miles they drive on local streets and roads, despite the fact that those taxes mostly pay for state and federal highway projects.
As for the numbers: According to the report, the amount spent on highways, roads, and streets has exceeded the amount raised through taxes, tolls, and other "user fees" by $600 billion since the interstate highway system was first built in the 1950s---"a massive transfer of general government funds to highways." Moreover, the report points out, most states exempt gas from state sales taxes, diverting those tax revenues to highways in the form of gas taxes. (This situation is even more pronounced in states, like Washington State, where gas-tax revenue can only be spent on highways.) As the report notes, "the shuffling that allows drivers to shift a part of their tax burden to a fund that largely benefits themselves is something extremely rare in our tax system. It is an exception—not the realization of some universally accepted principle of public finance."
In reality, user fees pay only about half percent of highway costs, down 10 percent in the past decade. The reason for this gap is that because state and federal gas taxes haven't grown at the rate of inflation, the total amount of gas taxes collected shrunk 32 percent between 1998 and 2009.
And then there's the factor highway proponents never want to talk about: Externalities, or the negative impacts imposed by drivers on society, including people who don't use the highway system. Those include the cost of accidents (injuries, deaths, property damage); air and water pollution from greenhouse gases and runoff; dependence on foreign oil; and sprawl. According to a 2009 study by the Victoria Transport Policy Institute, externalities make up fully 35 percent of the cost of driving.
Transit, in contrast, produces externalities that are almost entirely positive: Less congestion, lower emissions, less oil dependence, and smarter development patterns.
I'm not saying that transit "pays for itself" through user fees either---my $81 a month ORCA card is "subsidized" by sales taxes (which, by the way, I pay along with everybody else)---but people who claim drivers pay their way and transit riders don't are simply mistaken.