Tod Newcombe, Senior Editor of Governing's Urban Notebook, looks at the problem, and offers one potential solution.
Last year, when the "U.S. Experienced It's Second-Highest Transit Ridership Since 1957", commuter rail ridership increased .5% while total transit ridership jumped 1.5%. In addition, "10 out of 28 systems lost riders; decreases occurred at some of the newest commuter lines..."
As the American Public Transportation Association (APTA) report issued last March posted here notes, commuter rail was public transit's worst performer, behind light rail, heavy rail, and large bus systems.
According to Wikipedia, "Northstar runs 40 miles (64 km) from Big Lake to downtown Minneapolis at Target Field using existing track and right-of-way owned by the BNSF Railway. Extension plans are on indefinite hold due to insufficient ridership."
The other three lines noted by Newcombe saw significantly greater ridership losses. Rail Runner (Albuquerque, N.M.), Trinity Railway Express serving Dallas-Fort Worth, and Music City Star (Nashville, Tenn) saw ridership drops of 9%, 7.7%, and 6.4% respectively. For other commuter rail lines, some of which saw substantial ridership gains, see page 5 of the March, 2013 American Public Transportation Report (PDF).
Newcombe writes that the solution, though sounding "counterintuitive, involves more service", though he doesn't suggest building extensions. He points to the Metro-North Railroad, with ridership up 1.2% last year. "After watching ridership decline for decades on its line, the MTA added more off-peak and weekend service, as well as another 187 trains, representing the most ambitious service expansion in its 30-year history. As a result, ridership has grown robustly."
Freemark agrees with this strategy. “Too many of today’s commuter rail lines are wasted infrastructure. Can you imagine a highway where the lanes are only open during rush hour?”
Neither Newcombe nor Freemark address the funding challenge - each additional train the agency deploys amounts to a significant operational expense in labor and fuel, expenses not incurred by empty highway lanes. In fact, when budgets are tight, agencies will often seek to cut trains as well as raise fares.
An extreme example, a 44% reduction in service was proposed for Caltrain in the Bay Area two years ago. However, funds were found with the help of the regional transportation agency, and service was reduced by almost 10% instead. The train line's ridership increased a staggering 13% last year.