Mr. Trump’s budget suggested that new transit projects should rely on local financing — a major shift in how such projects have been financed in recent decades. Still, it is early in the budget process, and Congress will weigh in on the cuts in the coming months.

“These agencies count on a strong federal partner,” said Andrew Brady, senior director for government affairs at the American Public Transportation Association. “There has been a federal role in public transportation since Ronald Reagan put it there."

President Reagan signed a law in 1983 that raised the federal gas tax and reserved some of the money for public transit projects. The New Starts grant program was created in 1991 under the Federal Transit Administration, though conservative voices like the Heritage Foundation want to see it eliminated. Under Mr. Trump’s budget, only New Starts projects that have already secured full financing agreements would receive money.

But many transit agencies have already started planning new expansion projects. Some communities have approved local ballot measures to improve public transportation with the expectation that the federal government would provide matching funds. The list of transit agencies that are applying for federal grants is not confined to cities in the Northeast; it includes Phoenix, Indianapolis and Jacksonville, Fla.

Officials are moving forward with a $4.8 billion proposal to extend a train line west through San Jose, Calif., to the city of Santa Clara, said Stacey Hendler Ross, a spokeswoman for the Santa Clara Valley Transportation Authority. The agency is not “panicking yet,” she said, since it is early in the budget process. Officials plan to request $1.5 billion in federal funding.

“It’s such a strong project for the economic vitality of this region,” she said.

The trillion-dollar question is how Mr. Trump’s broader infrastructure proposal could affect public transit and how it would be paid for. The new transportation secretary, Elaine Chao, said recently that the initiative would be unveiled this year and that, in addition to transportation, it could focus on energy, water, broadband and veterans hospitals.