Latham is concerned that transit agencies will become reliant on the federal money rather, which disappears in two years, rather than finding sustainable local funding sources, or that the government will be prodded to pay for transit operations indefinitely. "There's nothing more permanent in government than a temporary program," Latham said.

Even with stimulus money newly available for operations, many transit agencies will be balancing services against long-needed upgrades. "Flexibility is welcomed," said Ted Basta, chief of business services for the Metropolitan Atlanta Rapid Transit Authority, "but in our case, it will be which house to rob to help the other side."

The deep trouble for transit agencies has been a decade in the making. Since 1999 [4], urban areas with more than 200,000 people have been barred from using federal transit funds to cover operating costs. President Obama's stimulus plan carried that theme forth by mandating that the $8.4 billion [5] in stimulus transit funds go only toward capital improvements, essentially construction, repair and new purchases, and not toward filling operating holes, like the $50 million deficit [4] that St. Louis Metro is facing.

When the transit provision becomes law, St. Louis Metro will be able to use $8 million in stimulus funds to cover a portion of the deficit, but it's not enough to restore all the decimated suburban bus service or the hundreds of jobs that were lost. In March, Metro closed 2,300 bus stops and cut 450 workers.

The stimulus money might be combined with $12 million in new state funds to bring back a third of the lost service. Meanwhile, some of the stimulus capital money will replace rail ties, according to Tom Shrout of Citizens for Modern Transit, a group that advocates expanding St. Louis transit. "That's fine," Shrout says, "but it doesn't have to be done now, and we'll lose riders for years if there's a service cut."

In New York, the state took evasive action to preempt a $1.8 billion deficit at the Metropolitan Transit Authority, which runs New York City subways and buses and suburban commuter rail lines. Still, the MTA had to boost fares about 10 percent even as it spent stimulus money on a subway line [6] that has been delayed for decades.

The MTA would not comment on whether funds, if they become available for operating costs, would be used to eliminate or reduce fare increases. But even if the entire 10 percent of allowable stimulus spending in the state of New York were used just to repair the MTA's deficit, it would not fill the hole.

Gene Russianoff, an attorney with the New York City Straphanger's Campaign, which advocates on behalf of transit riders, supports some of the MTA's capital projects. But he bemoans the loss of 570 customer service agents [7] in train stations. "The MTA [safety] slogan is 'If you see something, say something [8],'" he says. "But to whom?"

In desperation, some transit agencies have shuffled money around, trying to find any way that restricted state and stimulus funds can plug operating and maintenance holes.