Many flight routes cannot possibly exist if Earth is flat. Flat-Earthers showed the availability of the same routes with a stop to “prove” the non-stop routes do not actually exist. In reality, there are reasons airlines provide these routes with a stop, and some passengers do prefer to fly these routes.
The route with a stop can be far less expensive. Non-Stop-long-haul flight routes tend to be premium offerings and come with a price tag to match. On the other hand, flight routes with a stop at a hub tend to be much higher in volume, lowering the cost.
Non-stop routes might not be available every day. Non-stop routes between non-hub airports tend to be lower in volume and more difficult for airliners to fill. To accommodate this lower demand, they do not fly these routes daily.
A non-stop flight route contains two or more legs. To many airlines, these legs already exist, and all they have to do is make the connection, and make it available to the passengers.
The passengers might be frequent flyers of a specific airline and prefer to take advantage of the perks available. They might get discounts, free upgrades, free food & beverages, etc.