Their problem is that fare-box revenue accounts for only a fifth to a half of the operating revenue of most transit systems  and the sputtering economy has eroded the state and local tax collections that the systems depend on to keep running. “We’ve termed it the ‘transit paradox,’ ” said Clarence W. Marsella, general manager of Denver’s system, which is raising fares and cutting service to make up for the steep drop in local sales tax.

The billions of dollars that Congress plans to spend on mass transit as part of the stimulus bill will also do little to help these systems with their current problems. That is because the new federal money  $12 billion was included in the version passed last week by the House, while the Senate originally proposed less  is devoted to big capital projects, like buying train cars and buses and building or repairing tracks and stations. Money that some lawmakers had proposed to help transit systems pay operating costs, and avoid layoffs and service cuts, was not included in the latest version.

The Washington Metro set a record on Inauguration Day last month when people made 1.5 million trips on it to see the swearing-in of President Obama, but its $176 million budget gap means that it is planning to cut service and eliminate 900 jobs. Chicago had its biggest gain in riders in three decades last year, but was forced to raise fares. Charlotte, N.C., whose new light-rail system is the envy of transit planners around the country, and which is enjoying its biggest ridership levels since “the days of streetcars,” according to Keith Parker, the transit system’s chief executive, will be running its new trains less frequently, raising fares and cutting back on bus service.

In New York City, the Metropolitan Transportation Authority is considering steep fare increases and its deepest service cuts in years to help close a $1.2 billion deficit. In addition to considering a 23 percent increase in fares and tolls, the authority is weighing plans to eliminate more than two dozen city bus routes and two subway lines, reduce off-peak service and even close some subway stations at night.

The nation’s transit woes threaten to deal another blow to the weak economy, keeping some workers from jobs they commute to and forcing some systems to lay off administrators, bus drivers, train operators and mechanics. And while the economic stimulus package being considered on Capitol Hill includes tax cuts intended to put more spending money in people’s pockets, fare increases promise to take a big bite for many commuters.