The Bay Area’s newest transit system — Sonoma-Marin Area Rail Transit or SMART — rolled to a start Friday, cheered on by hundreds who attended a morning ceremony and then waited in line to ride the green-and-gray trains as they made their way from Santa Rosa to San Rafael.

SMART has faced controversy since it was little more than an idea, but the arrival of the trains, which promises to ease Highway 101 congestion in the North Bay, was greeted with excitement and happiness — emotions not usually associated with a commute.

“It was great,” said Elizabeth Cargay, 55, a geologist from Windsor, as she stepped off the first southbound train in downtown Petaluma. “It went a lot faster than I thought it would. It was smooth, it was clean. It’s great to finally have it.”

The new rail system’s opening day began in the morning at the downtown Santa Rosa station in the town’s historic Railroad Square, where a crowd grabbed SMART memorabilia, including squishy miniature trains, plus snacks and coffee they may have needed to sit through 12 speeches by politicians and SMART officials.

Later in the day, passengers were treated with free rides along 43 miles of new rails.

During the morning ceremony, speakers praised taxpayers for funding construction of the service and the SMART staff for persevering through nine years of challenges after voters in Sonoma and Marin counties approved a quarter-cent sales tax in 2008 to pay for the system.

Those challenges included a failed effort to repeal the sales tax, feuds over station locations, mechanical troubles with the new locomotives and, finally, an extended wait for federal approval of SMART’s train control system, designed to prevent head-on collisions and accidents caused by speed.

The Federal Railroad Administration gave the go-ahead on Aug. 17, and SMART officials quickly set Friday as the opening date.

“This is really happening, isn’t it?” said Rep. Jared Huffman, D-San Rafael, as he spoke from a podium on the downtown Santa Rosa station platform. “Starting today, all of us are actually going to start using the SMART train.”

Rides were free on all SMART trains Friday, and through Labor Day, they’ll be half price. After that, one-way fares, payable by Clipper card or a smartphone app, will range from $3.50 to $11.50.

The big question is how many people will ride SMART trains once the rail system is no longer a novelty. In July and August, free preview rides drew standing crowds, as did Friday’s first train, which departed the northernmost station near Sonoma County Airport at 12:49 p.m. — just as scheduled.

A few eager people arrived at the station more than two hours before departure to make sure they had a seat on the first passenger train to travel through Marin and Sonoma counties since 1958 when the Northwestern Pacific Railroad ground to a halt.

Scott McLaughlin, 55, an appliance repairman from Santa Rosa, had the day off, so he decided to give the train a try. He was first in line, arriving at 10:30 a.m. at the Sonoma County Airport station, which is about a mile down the road from Charles M. Schulz airport.

“I’ve been paying for this for years with my taxes, so I thought I’d see what it’s like,” he said.

McLaughlin said he expected a smooth ride, having seen crews install new rails and concrete ties.

“I don’t think we’ll hear a lot of clickety-clack, clickety-clack,” he said. “I think it will be a very smooth ride, not very jerky.”

He was right. The three-car train hummed as it rolled, mostly smoothly between Santa Rosa and Petaluma, picking up more passengers at each stop, some of whom roamed the aisles.

Every SMART train offers a restroom, a cafe that serves snacks and beverages, including beer and wine, and hooks for bicycles. Some of the light-green upholstered seats are arranged around tables and the rest have tray tables, and recline, like those on an airplane but with more legroom.

Many of the first-day riders were either retired or on vacation, and said they’d ride SMART but not regularly.

“I’ll just use it for fun,” said Charlotte Laverty, 68, of Santa Rosa. “But if I really have to get to San Francisco, I will probably hop in my car.”

SMART’s big test will start Monday when commuters give it a try and decide whether they prefer it to sitting in their cars on Highway 101.

SMART isn’t done. It plans to start construction of an extension to Larkspur, within walking distance of the Golden Gate Ferry to San Francisco, within weeks. But until then, riders will have to take a free shuttle bus. And it also has plans to extend north to Windsor, Healdsburg and Cloverdale.

If first impressions count, the train was a hit with David Minard, 31, a photographer from Santa Rosa.

“It’s pretty much better than the freeway,” he said. “But it will be much more useful once it gets to Larkspur.”

Michael Cabantuan is a San Francisco Chronicle staff writer. Email: mcabanatuan@sfchronicle.com Twitter: @ctuan