I went to the one in West Palm Beach (years ago) and thought it was a neat one-of-a-kind place. I was also a little disappointed to find out it was a chain.
We had one near me (suburbs of Baltimore) when I was younger, and never knew it was part of a chain. IIRC, that one just closed. It’d been there forever.
I also didn’t know until maybe a year ago that the 94th Aero Squadron was a chain. I think I learned that here on the SDMB. I went to the one in St. Louis on a date when I was in high school. I thought I was taking my girl to a super nice place. Oops. The one in St. Louis was near the airport, and part of the attraction was watching the planes. It appears to be closed now. Are they all near airports?
Yes. From looking at their website, it looks like there are just four left; one in Van Nuys, CA, one in Miami, FL, one in Wheeling, IL, and one in College Park, MD. They’re all next to airports.
I didn’t realize that Bensi was a (regional) chain until I looked at their take out menu. Good food for relatively cheap, and nice decor.
When I was a tiny little kid (back in the 70s), I didn’t realize that Red Lobster was a chain. More recently (well, within the past 15 years), it’s been Joe’s Crab Shack. Apparently it’s only seafood place that confuse me. 
A couple of years ago (Late 80s) my family was driving through NH and we got lost.
My mother gets shrewish when we’re lost, and my father just gets quiet. And then things get worse when she goes hypoglycemic. So, it was out of desperation that we stopped at what seemed to be a local watering hole in Ashland, NH: The Common Man. We sat down in a tense silence, and looked at one of the more interesting menus we’d seen in ages.
The bread rolls were awesome, and by the time the meal came around we all felt we’d been blessed to have stumbled into this place. Not only was the food awesome, but it had created peace in our family - a true miracle after the rest of that afternoon.
Then we had dessert: I had the cheesecake, and my mother and sister had the white chocolate mousse.
I don’t get why people rave about The Cheesecake Factory. They’re good. But they are not ambrosia. Not perfection. My mother was so impressed with the mousse that she asked for the recipe and it’s become a staple for her and my sister around the holidays.
It was another ten years before I realized that it was part of a growing local chain. (My family had kept vacationing in NH without me, and so found out long before that.)
WW I-themed
It looks like the 94th Aero Squadron restaurant in San Diego off Montgomery Field is still in operation. It wasn’t listed on the corporate website but Googling shows numerous recent SD (Kearny Mesa) mentions. Perhaps this location split off from the main company but retained the name. I haven’t been there in years but my family went there frequently.
This is my 99th post, I better come up with a good one for my 100th 
I ate at Pizzeria Due back when it was the only branch of the original pizzeria Uno. It’s across the street. Shortly after I ate there, they opened the first franchise in Boston.
I ate at Regina’s in Boston’s North End before it became a (fairly local) chain.
I also went to the original Steve’s Ice Cream in Somerville, MA before they became a chain that stretched across the country (there was one outside the University of Utah when I was there). Then it shrank back to nothing – the orighinal Steve’s isn’t there anymore.
In fact, I can’t think of any place that I thought was a single restaurant, but was actually a chain. But i HAVE eaten in single restaurants that became chains.
Puccino’s. I went to a coffee bar with quirky messages on the walls in Oxford. Didn’t occur to me that it could be anything other than unique until I spotted one in a railway station in London.
There is a Canadian pizza chain called Boston Pizza which was founded in Alberta and AFAIK has no connection to the city of Boston 
Too bad you didn’t make it five posts ago. 
Boston Market started as Boston Chicken (before they expanded their menu), and at ione time there WAS only one, on Boylston Street. I ate at it one time, and wasn’t impressed.
Their food got better, and they expanded. It’s OK, but it IS a chain.
I’m a bit puzzled by your wishing Popeye’s was still around – the chain IS still around. In fact, there’s one on Boston, not far from Fenway Park.
I’m guilty. Until this thread I too thought Bucco di Beppo was a local Sacramento place. Huh, kind of takes some of the charm out of it. Still, can’t beat dinner at the kitchen table though.
If you like one, you’ll like the other. I’ve eaten at both numerous times, and they’re using the same model.
Macaroni Grill. If that counts.
OtakuLoki, we love the Common Man! Loved the Squam Lake Seafood Company, too, while it lasted :(. I just checked out the web site; haven’t been there since “Foster’s Boiler Room” opened. I always wanted to go to Camp.
I don’t think OUR Mimi’s is part of a chain!
But for my own nominees, I did a double-take the first time I saw a(nother) Abitino’s Pizzeria. Totally thought it was a mom-n-pop establishment. Likewise Rosa Mexicano (“Hey, that restaurant’s got the same name as…”)
I ate at Au Bon Pain (awful, just really bad) before realizing it was a chain.
I’m not sure if I knew Panera was a chain when I tried it. More than anything it reminded me of Au Bon Pain. Lousy.
Someone I know can’t help but say “Ow! Bone pain!” when he sees one…
Joe
The Old Spaghetti Factory. I grew up in the Seattle area, and they were located in a funky old building on the waterfront, so I had assumed it was a unique place.
Until I moved to Minneapolis.