It took Josh Hunter three separate planes, two connections and a two-hour drive to get from Mobile, Ala., to Cincinnati at Easter. When he added it all up, his 720-mile trip had lasted 12 hours — about the same it would have taken him to drive.


“The whole point of flying should be to save a lot of time, and I didn’t,” Mr. Hunter said.


For anyone trying to fly between the smaller cities in the United States, it’s not easy to get from here to there anymore.


The major airlines have been paring service for much of the last decade. But their cutbacks accelerated three years ago as carriers merged, fuel prices spiked and the recession reduced demand for seats. Even after the economy started to recover and passengers came back, the big airlines did not restore many of their flights, particularly on routes to small airports, as they sought to bolster their profits.


The strategy has squeezed the regional airlines, whose purpose is to ferry passengers on behalf of the major airlines and provide the backbone of air service to the nation’s small airports. Three regional carriers have filed for bankruptcy protection since 2010, including Pinnacle Airlines in April.


So while airports in large metropolitan areas like New York, Chicago and Atlanta have emerged relatively unscathed from these changes, the smaller cities have borne the brunt.


From 2006 to 2011, the nation’s top 25 airports lost 4 percent of their nonstop domestic capacity, according to Jeffrey Breen, the president and co-founder of the Atmosphere Research Group. In that same period, the next 25 airports, among them Oakland, Calif., and Kansas City, Mo., lost 13 percent. At the next 50 airports — places like Tulsa, Okla.; Providence, R.I., and Reno, Nev. — the drop in direct service was even steeper, 15 percent. Smaller airports, like the one in Flint, Mich., have fared even worse, down 19 percent.


“We are all in the same boat here: most airports have lost nonstop capacity in the last five years,” Mr. Breen said. “But the smaller airports are really the ones that have taken it on the chin the most. It’s been a perfect storm for them.”


The result is that travelers now face more complicated itineraries, often involving a connection at a big hub airport, and trips that used to take two or three hours can now stretch all day.


Fares in the smaller cities have also risen the most. Ticket prices out of Bellingham, Wash.; Harrisburg, Pa.; and Fort Myers, Fla., for instance, jumped 16 to 18 percent from the third quarter of 2010 to the third quarter of 2011, while the average nationwide increase was 6 percent, according to the latest data compiled by the Bureau of Transportation Statistics.


The three most expensive airports to fly from? Cincinnati (where the average ticket price was $488 in the third quarter); Huntsville, Ala. (average price $473); and Memphis ($472). The nationwide average ticket price was $362. (And none of this includes extra fees for checked bags or seats with extra legroom, which have also been rising in recent years.)


“Smaller airports have taken the brunt of the fare increases over a long period of time because they lack the kind of competition that tends to drive down prices,” said Rick Seaney, chief executive of FareCompare.com, which tracks ticket prices.


The regional airline industry once enjoyed explosive growth, starting in the 1990s. The number of passengers flying on regional jets doubled from 1990 to 2000 and doubled again from 2000 to 2010. Regional jets still account for half of all domestic flights, though because those jets are smaller (on average, just 56 seats), they carry only about a fifth of all domestic passengers.


The regional business was profitable because airlines used them extensively in exchange for a fixed fee per flight. But as the big carriers looked to cut costs, they renegotiated their deals with their regional partners. With little control over their own schedules and routes, and with fuel prices rising, these smaller carriers have struggled. Many routes, particularly those on 50-seat planes, are no longer economical.


“The regional model,” said Helane Becker, an airline analyst at Dahlman & Rose, “is broken.”