I believe it goes back to the early days of CRS's. Flights were listed on a travel agent's screen with non-stops first, then single-flight-number multi-stops, then finally connections.

I first noticed this sometime in the 80's on DL. Their schedule listed a one-stop DTW-HNL, which was really their normal morning 727 DTW-DFW, connecting to an L10 DFW-HNL, but with a single flight number assigned to the combination. A little research revealed this one DFW-HNL flight was part of 6 or 8 "direct" flights from places such as CLE, MSY, PIT, etc. Sneaky, but I'm sure it got DL to the top of the CRS screens, so it accomplished their objective.

Now, of course, probably 80% of alleged direct flights aren't intended to be run with one aircraft, but are just disguised connections, which will surprise infrequent flyers, especially the elderly and the disabled, who might book one of these flights thinking they can go, say, PVD-MSY without having to run the length of a terminal.