Coming from a supposedly “pro-transportation” governor, the proposed budget of Dannel Malloy has a lot of transportation advocates confused.

“It’s hard to follow the dollars here,” Joe McGee, of the Business Council of Fairfield County, said Wednesday afternoon.

“I work with these numbers all the time. I know these budgets. And I’m confused. What am I missing?”

On the one hand, Malloy’s budget calls for a $1.26 billion special transportation fund for the coming fiscal year. Transit advocates have also been heartened by the work on the Hartford-to-New-Britain busway and the New Haven-Springfield high-speed rail line.

On the other hand, transportation — like all other state services — faces steep cuts as the administration tries to claw its way out of a several-hundred-million-dollar budget hole. And though next year’s proposed spending is about $42 million above current levels, it falls $90 million shy of the level needed to maintain current services, according to nonpartisan legislative analysts.

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Breakdown of state transit funds. (From 2013 report by state Office of Fiscal Analysis)

The special fund supporting Connecticut’s highways, bridges and railways would be raided for non-transportation programs under Malloy’s proposed budget, continuing a trend that began roughly a decade ago.

Two days earlier, Republican state Rep. Gail Lavielle of Wilton had suggested changing state law to convert the roughly $1.3 billion fund into a “lock box” that could not be used for other purposes.

“If you don’t do something to make some structural changes to the budget to leave money to spend on transportation, I fear for the consequences,” Lavielle said. “We have trains that are unsafe, we have bridges that are unsafe.”

While campaigning for governor in 2009, Malloy promised to preserve the Special Transportation Fund. In 2011, he tried, shifting $30 million away from the general fund and into transportation.

But as state finances have fallen into deficit, things have swung the other way. About $70 million was taken from transportation and put into the general fund this year, and Malloy wants to take another $75 million next fiscal year.

“He has broken his promise regarding the transportation fund for the second budget in a row,” one of Malloy’s chief critics, Senate Minority Leader John McKinney, R-Fairfield, said Wednesday.

Car, bus commuters asked to give more

Malloy’s budget also assumes a major increase in the wholesale tax on gasoline and other fuels signed into law in 2005 by Gov. M. Jodi Rell. As far as motorists are concerned, about 3.8 cents per gallon will be added to the price of gasoline starting July 1, and the state expects to collect an extra $32 million next fiscal year.

Malloy spokesman Andrew Doba responded to McKinney’s charge Wednesday, saying, “Governor Malloy has proposed a robust investment agenda for our state’s infrastructure projects, as inconvenient as that may be for the senator.”

The transportation fund expects to close this year with a $159 million reserve that is projected to grow to $164 million next year.

“Most residents, at least those not running for governor, would think taking surplus funds and using them to address what would be painful cuts that would affect our most vulnerable, is just common sense,” Doba said.

But those reserves apparently will not be used to offset other cuts that many say will hurt the state’s poorest residents, as well as worsen its already crumbling infrastructure. Bus fares will jump under the proposal, and many commuters with disabilities will also be asked to pay more. The state’s rail budget will be cut by $2 million, and expenditures on road maintenance for towns will be shifted to the state’s credit card.

“Those have consequences,” said Steve Higashide, of the advocacy group Tri-State Transportation Campaign. “It feels like few areas were spared in this budget, and transportation wasn’t spared either.”

Lavielle was also concerned that the rise in fares for bus riders and riders with disabilities were going toward filling in the state deficit, rather than improving the transportation system. She has proposed separate legislation that would prevent this.

“If you are collecting money off rail and bus fares, that money should be used for rail and for buses,” she said. In recent years, the legislature has also raised fares for Metro-North riders, with the increase in revenue going toward the state’s general fund rather than the rail system.

Ben Barnes, secretary of the state’s Office of Policy and Management, said it was incorrect to assume that increases in bus fare would go toward services other than transportation. But nowhere in the proposed budget is that made clear.

“Is the money raised for transportation staying with transportation, or is it being used to cover part of the deficit? It’s unclear to me,” said McGee of the Business Council of Fairfield County.

A ride on the public bus costs $1.25 right now. Under Malloy’s plan, it’ll go up to $1.50 in 2014 and raise $4 million next year. For riders with disabilities that prevent them from riding regular public transit, they’ll have to pay 4 percent more to ride what are known as paratransit vans provided for them under federal law.

Advocates say the fare increases will impact commuters who are already suffering.

McGee credited Malloy for continuing to focus some investment in transportation, but he questioned whether Connecticut has an overall comprehensive plan.

“We know he’s committed to transportation. But it’s confusing,” McGee said. “[W]e are not clear exactly on what his intentions are.”

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