An airline just for pets was an act of genius, Martha Hamilton figured. No cold cargo holds for Phoebe, her 10-year-old miniature schnauzer. Attendants would check on her regularly during the flight. There would even be a pet lounge for the emotional goodbye at the airport.

But Ms. Hamilton and Phoebe just finished a three-day cross-country journey — in a car.

The once-loved Pet Airways, created by a California real estate developer, has run into trouble, stranding cats and dogs and leaving their unhappy owners holding the leash.

“It’s outrageous,” said Ms. Hamilton, after Pet Airways canceled three reservations. “Thanks to Pet Airways, I had to fly from New York to L.A., rent a car and drive all the way back.”

Pet Airways — once the great transportation hope for animal owners — is now suffering a fate similar to its counterparts that cater to human travelers.

Dog and cat owners are angry about canceled flights. Travel sites are abuzz with complaints, including customers who claim they have not received refunds for paid-for flights. And the company is burning through cash at a rapid rate.

The co-founder of Pet Airways, Alysa Binder, acknowledged in an e-mail exchange that the airline, which does not own an airplane, has had some problems since November, when it decided to contract a plane from a new company. “After several flights, it was apparent that the company and plane could not perform as represented, and that there was a definite safety issue, especially in cold weather,” said Ms. Binder.

Pet Airways, she indicated, has since switched back to its previous contractor, but needed to cancel “some flights during the holidays and into the new year” because that plane was committed elsewhere.

“We are a very new company that is pioneering, just as FedEx pioneered the overnight packaging business,” said Ms. Binder. “We have ups and downs, but we are keeping our eyes on the long-term goal of providing a safe and comfortable transportation option for the pets.”

Begun in July 2009, Pet Airways held great promise. Frustrated by their experience traveling with their Jack Russell terrier, Zoe, Dan Wiesel — a former real estate developer and women’s swimwear manufacturer — and his wife, Ms. Binder, wanted to offer a better way.

“We got to thinking. Maybe Zoe was trying to tell us something,” the two, who own roughly 37 percent of the company, wrote on the company’s Web site. “Maybe there was a travel solution that would suit her perfectly, and everyone else out there too.”

In the beginning, the upstart, which offers service to nine cities including East Farmingdale, Long Island, trumpeted better service at a potentially lower cost than traditional carriers. Flights run from about $100 to more than $1,000 each way, and roughly 40 pets can sit in crates in the main cabin (the airline doesn’t carry the pets’ owners).

“Your best friend travels in four-legged style in the main cabin, constantly monitored by a pet attendant with the temperature just right and with lots of fresh circulating air,” boasted an online commercial.

Since the service began, Pet Airways says, it has flown more than 7,000 cats and dogs, and at least one potbellied pig.

It was an upgrade from the alternative. Major airlines — some of which ban even small pets in the cabin — typically store animals in the belly of the plane with luggage and other cargo. There, the temperature can vary wildly, leading to death in rare cases. Between May 2005 and July 2010, 122 dogs died in cargo holds of United States airlines, according to the Department of Transportation.

Now, Pet Airways has fallen on tough times. The carrier — which based on its recent schedule typically offers two eastbound routes a month and two westbound ones — did not have any flights between Dec. 16 and Jan. 16, according to a regulatory filing, and it is unclear if it has had any flights since then. A New York Times reporter looking into the airline had reservations canceled twice, once in January and another last week. Her credit card company canceled the charge.

Ms. Binder declined to comment on the last time Pet Airways operated a flight. The airline continues to take reservations. “We are working toward being in the air as soon as we can be assured that the planes are ready for our use,” Ms. Binder said.

But its financial picture also looks shaky. At the end of the year, the company had roughly $30,000 in cash on hand, and its “net monthly cash burn” is $25,000 to $55,000 a month. In the filing the company said it did “not currently have sufficient cash on hand to meet our financing needs.”

“We have experienced a history of losses and have yet to begin generating positive cash flows from operations and, as a result, our auditors have raised substantial doubt about our ability to continue as a going concern,” the company wrote in the February regulatory filing.

The situation has left this special breed of fliers without many options. Colleen Paige — who rescued an 8-year-old longhair German shepherd named Rocky in Los Angeles and secured a home for the dog in North Carolina — said Pet Airways had canceled on her twice. Now, it’s unclear where Rocky will end up.

“They won’t call me back,” she said of Pet Airways, which has not yet refunded her money. “Rocky is with a foster family who can’t keep him indefinitely.”