Many subway riders in the New York City area sense a certain decay settling in as the system continues to suffer from age, budget limitations and problems related to Hurricane Sandy. The Straphangers Campaign — activists who have been assessing mass transit for 35 years — confirm that unease. The group estimates that the subways have shown a “significant decline” in cleanliness; fares have gone up steadily; crowding is getting worse.

The enduring problem is that the Metropolitan Transportation Authority, which manages mass transit in and around the city, is constantly struggling to pay its bills to operate commuter rail lines, bridges, tunnels, buses and subways.

Yet Gov. Andrew Cuomo’s latest budget proposal would skim $40 million from a fund partly dedicated to providing much-needed dollars to mass transit.

These dedicated funds flow from various sources, including a small percentage of the sales tax in downstate areas and some of the tax on real estate transactions. Last year, Mr. Cuomo’s office lifted $20 million from the fund, after which Assemblyman James Brennan, a Democrat from Brooklyn, tried to stop the raid with a bill designed to insulate the money and require that it be spent for transit. The bill passed both chambers, but Mr. Cuomo vetoed it. The governor’s supporters argue that he has increased financing for the authority every year and that $40 million is not much in the agency’s $13.6 billion operating budget. But every dollar lost means the agency has to scrimp.