This is my answer, but in reverse. Returning from Italy, we did customs in Miami, flew to Indianapolis and then a handful of us switched to a small plane to finally hit Chicago.
Some years ago, some radio station was promoting a contest related to the Crosstown Classic (Cubs playing the Sox) where you could win a jet ride from Midway to O’Hare. I don’t remember the details but recall that it was on a commercial airliner versus some small private plane.
Technically, the smallest ‘commercial’ plane I’ve been in was a Cessna 150 (two seats). Dad rented it. As a rental, it was in ‘commercial’ operation.
The smallest ‘commercial’, as in Part 135, airplane I’ve been in was a six-seat Cessna 206 from Bellingham to Orcas Island (about 20 miles).
I have many times taken the CVG to DAY flight. It is 64 flight miles or 78 miles driving. Delta had some pricing scheme that made it several hundred dollars cheaper to fly through Cincinnati than to fly directly to Dayton, which was my final destination.
I’d also take the DAY to CVG flight on the way out for the same reason. It must have made sense to someone, but I don’t know why.
Driving to Orcas Island is a 62-mile drive, taking about 2½ hours and requiring queuing up for a ferry and taking the ferry over. It’s much nicer to fly over in a few minutes. 
I believe it was from LA to Orange County in about a 20 seater. I remember walking up the stairs to the plane and the pilot announcing “Welcome to our new passenger from Los Angeles” while all the other passengers looked at me as if to say " So you were the reason we had to make this extra stop!"
I think short flights in small planes are pretty common in the Caribbean. I spent some time waiting for my flight out of SJU and noticed the little tiny planes lining up for launch. I think you can pretty much get a flight to nearly any island in the Caribbean out of there - except for Cuba.
My shortest trip was from Kinshasa ( Democratic Republic of Congo ) to Brazzaville ( Republic of Congo ). The straight line distance is about 6.2 km ( 4 miles ) and I was on a Sabena 747.
The elapsed time - takeoff to landing - was 40min and the flight cost around USD 400 ( I was in Business Class ).
What was the flight path that a 4 mile flight took 40 minutes? I can see boarding to deplaning taking 40 minutes, but the flight itself should have taken only a few minutes even accounting for climbing and descent.
Houston Hobby to Houston Intercontinental several times. Part of the booking for flights I made during the 80s while living there was an option to catch the jet from the big airport, or save the car travel and prop up to the big one from the south side Hobby airport. Always flew Continental then.
Having the option of a short taxi (or friend) ride to the closer airport vs driving and parking much further north was nice. I lived in the Friendswood/Pearland area.
I got curious. It was an Airbus 320 provided by TED (United)
Shortest over all for me was Ontario CA to LAX. I was flying from Minneapolis, and my ticket said direct to LAX, but we stopped in Ontario and EVERYONE else got off. Me and the flight crew went on to LAX. Boy those big jets can move when they are empty! Never found out what that was all about.
Shortest scheduled was Chicago to Madison WI. Ascending and descending times were 90% of the flight.
Smallest plane was a high winged turboprop (which I can’t remember the manufacturer or model) that seated something like 20. It was an “efficient” design - the fuselage was squared off rather than cylindrical. Made more room inside.
I took a puddle jump flight from Mason City, IA to Waterloo, IA once. Distance 83.5 miles. It was a long time ago, before TSA. I have no idea what the plane was, other than being a prop, I think. I remember seeing the propellers. Capacity was 15 passengers, one on ea side of the aisle. I believe we were close to full that day, maybe 12 total. We all walked out to the tarmac and climbed aboard. The pilot climbed on board after us. He was wearing a Budweiser tee-shirt and jeans. There was no co-pilot or steward or any of that fancy schmancy citified stuff. We took off in the middle of a blinding thunderstorm, with lightning flashing all around the plane. We made it there ok, but I vowed I’d never do that again. I don’t know what bothered me more - the weather or the fact that the pilot was wearing a Budweiser shirt!
Shortest was from LAX to Orange County airport. It was so stupid. It was a business trip and someone set it up for me. Fly Chicago->LA->edge of LA.
Smallest was an airplane designed to land on a short runway -the island of Saba’s airstrip. I don’t remember what kind of plane it was, but I think the passenger seating was about 8 or 10.
I once took a flight from Boise to Spokane which, due to the time zone change, landed two minutes before it took off.
Ketchikan to Metlakatla is something like 20 miles. I think I’ve flown shorter distances but most of those were charter and not scheduled service.
Cessna 185, They say it seats 6 but more like 4
San Juan to Beef Island = 95 miles, 49 minutes
San Pedro Sula to Roatan = 110, 50
Nassau to Treasure Cay = 118, 35
Madison to Milwaukee = ? No airlines fly that route any more but it was pretty dang short.
Shortest international flight I’ve taken is Tel-Aviv (Ben Gurion Airport) to Amman, Jordan which seems to be about 60miles/100km. It still took 45 minutes in the air though, mostly because it had to swing out to the east to land.
In the 00’s Continental still ran a shuttle from Ellington Field in southern Houston to Bush Intercontinental in northern Houston. Distance as the crow flies of about 30 miles. I took it several times, since it was an incredible deal–it was free, parking at Ellington was free, security at Ellington was a lot easier to get through, and you got something like 500 frequent flyer miles.
Needless to say, they ended that eventually.
Many, many moons ago, I was editor of a lifestyle magazine for the Florida Keys. One of my freelance writers in Key West interviewed a bi-plane company that operated on the island there. As a perk for running the story, the company offered to give magazine staff a free ride. So the writer set it up for me and my art director.
I think this counts because people have to pay for these rides, although I didn’t. Therefore, it was a commercial airplane. The ride was approximately 15-20 minutes, but I could have gone several hours. My friend wouldn’t let the pilot do loop-de-loops or this would be a better story.
I did Indy to O’Hare on a full-size American Airlines 727. That’s 164 miles. They even offered beverage service, which I’m sure thrilled the flight attendants.
<100 mile flights I’ve taken include:
Minneapolis-St. Paul to Rochester, Minnesota (41 miles)
Lexington, Kentucky to Louisville (68 miles)
Lincoln, Nebraska to Omaha (77 miles)
O’Hare to Janesville, Wisconsin (92 miles)
Baton Rouge to New Orleans (94 miles)
I was scheduled to take a flight from Madison, Wisconsin to Milwaukee (75 miles) but we ended up closer to Milwaukee and cancelled that leg of the trip.
