Getting to work is an odyssey for Shaun Ralston.

It starts at 6:10 a.m., when he mounts a bike outside his granny flat in Santa Rosa and rides 2 miles to the SMART train station. He boards a train as the first pink sunlight washes over the clouds, rides down to San Rafael, and transfers to a bus that crosses the Golden Gate Bridge and glides into San Francisco’s Financial District around 8 a.m.

One trip, three modes, two transfers. But before the train started rolling two years ago, Ralston drove or rode a bus along the painfully sluggish lanes of Highway 101. He said the SMART train, which is now dogged by financial trouble, has changed his life.

“It’s just so much better than bumper-to-bumper traffic,” he said, sitting with his laptop on the train, as the green hills of Sonoma and Marin streaked by. He’s looking forward to the opening of a new station near the Larkspur ferry terminal in December, a hard-fought victory that will bring North Bay commuters one step closer to San Francisco.

The $600 million Sonoma-Marin Area Rail Transit line, envisioned as a fast-moving alternative to the traffic on Highway 101, is struggling with mounting costs and a dearth of sales tax revenue. Unlike BART, it’s a small, boutique service with no rush-hour crowds. But those charms also create a quandary for the system as it tries to develop a ridership base.

SMART will deplete its funding reserves by 2024 if voters don’t renew a quarter-cent sales tax to keep the trains running. Its fare box recovery rate — the amount of revenue divided by the operating costs — is 10%, far lower than BART’s rate of 73% or Caltrain’s rate of 66%.

The system’s top official is relentlessly optimistic, characterizing SMART as a nimble startup that’s enjoyed some early success: This month it beefed up some trains from two to three cars, while clinching an Excellence in Transportation award from the state, and it’s on the verge of opening the new Larkspur station.

Eventually the railroad’s board of directors and managers want to grow east along Highway 37 to connect with Amtrak’s Capitol Corridor in Solano County. For now, though, they have a more immediate need: passing a March 2020 ballot measure to extend the sales tax and prevent service cuts. The board would have to approve the measure this fall to put it before voters.

“Look, BART is 47 years old; Caltrain is 150 years old,” said General Manager Farhad Mansourian. “We’re 2 years old. We’re only getting cuter and bigger and better.”

SMART has always specialized in “the art of the possible,” said Jeffrey Tumlin, a principal at the San Francisco transportation consulting firm Nelson\Nygaard. Funded with a quarter-cent sales tax that began in 2009, it sought to build a 70-mile track from Cloverdale to Larkspur, with a bicycle pathway linking stations.

It used a railroad that already existed, though the tracks lay dilapidated after Northwestern Pacific stopped transporting passengers 60 years ago. The railway lured in a few companies and generated three transit-oriented development projects in Rohnert Park, Petaluma and Santa Rosa, setting off a new pattern of land use in the sprawling North Bay.

Even so, SMART lays bare the conundrum of building rail in the Bay Area, particularly in the rural, sparsely populated towns and suburbs of Marin and Sonoma counties.

It’s a bigger, riskier investment than a well-run bus system, which could accomplish the same goal of relieving congestion and getting people onto mass transit at a much lower price. Yet taxpayers are more inclined to fund trains than buses, and rail is better at initiating new development than any other form of transportation, if cities are willing to rezone the land.

Whether SMART will reap those benefits is unclear. The train, while appealing to Wine Country tourists and commuters who want to escape choked freeways, is also hobbled by its design. It doesn’t run through a major job center or connect directly to San Francisco; anyone traveling across the bay might have to make two or three transfers.

About 2,800 people ride the train each weekday, in line with projections, Mansourian said, but nowhere near the 400,000 passengers that BART serves. SMART aspires to be a robust commuter rail but at this point runs small trains with big gaps in service. Its scenic route — past barns, through hills and over wetlands, with not an apartment building or office tower in sight — illustrates a key challenge for the rail system.

Still, it beats driving, said passengers who boarded the train in downtown Santa Rosa at 6:31 a.m. Tuesday.

“I do the drive on 101 too, which is enough to rip anyone’s hair out,” said Kathleen Borie, a finance worker who rides the train a couple times a month from her home in Santa Rosa to an office in San Francisco.

Like other passengers, she praises the amenities: upholstered seats, luggage racks, a coffee bar and Wi-Fi. Some segments of the railroad run directly parallel to Highway 101, including an agonizing stretch called the Marin-Sonoma Narrows, where the freeway shrinks from four lanes to two. Widening projects have been under way for years and aren’t expected to be finished until 2023. When SMART riders see the Narrows whoosh by through their windows, they often clap.

“For people who no longer have to sit in their car for two hours at the Narrows, it really is a world-class system,” said Shirlee Zane, a SMART board director and Sonoma County supervisor.

But the railway hit problems almost immediately. First came the economic recession beginning in 2007, which caused sales tax revenue to dip. Construction costs soared. The agency’s expenses outstripped its revenue from year to year, and officials began chewing up reserve funds to fill the gap. SMART had placed a 2029 expiration date on the sales tax to make it more palatable to voters, but now officials say that ending the tax after 20 years was never a viable plan.

So, SMART is touting a new one: Renew the sales tax, refinance the debt and save about $12 million a year. Rail officials would leverage their sales tax earnings to get state, federal and regional grants. They managed to bring in $300 million that way during the first phase of the build-out, doubling the railroad’s sales tax revenue.

There is no guarantee that voters will extend the sales tax. They defeated it before — the measure lost in 2006 before achieving the two-thirds threshold in 2008 — and this time, it may wind up on the ballot alongside a separate sales tax in Sonoma County for fire prevention.

Sales taxes are the lifeblood of public transportation in the Bay Area. Even if SMART were to raise fares and cut service, it would “unequivocally” have to shut down if the tax expires in 2029, said Randy Rentschler, legislative director of the Metropolitan Transportation Commission.

Mansourian won’t even acknowledge that possibility.

“There is no mode of transportation that doesn’t require some kind of tax,” he said. “We have a quarter-cent sales tax, and we’re not going to increase it. We’re only asking voters to extend it.”

Mansourian and other officials are already thinking about the next expansion for SMART: new stations north of Santa Rosa in Windsor, the Wine Country capital of Healdsburg and Cloverdale. Every addition is transformative for commuters like Ralston, who sat in a traffic jam Tuesday, right where 101 dipped into San Francisco. It was the last leg of his journey.

“This is why I don’t like driving to San Francisco,” he said, sighing. “No matter what mode of wheeled transportation you take, you’re stuck in this.”

Rachel Swan is a San Francisco Chronicle staff writer. Email: rswan@sfchronicle.com Twitter: @rachelswan