Pricing is primarily based on what an airline feels the value is of travel between your starting point and your final destination. How you get there is a secondary consideration.
If there is a large supply of unsold seats on the nonstop flights, then those tickets will likely be cheaper than flights with connections.
If there is a small supply of unsold seats on the nonstop flights, then those few remaining tickets will likely be more expensive than flights with connections.
These prices will change up or down based on how many tickets are sold as you get closer to departure time.
Something I haven’t seen is that Hubs allow for much more flexibility in case of irregular operations.
Like, just looking at Las Vegas to Cincinnati as an example, Delta operates a single flight each day, leaving LAS at 11:15 PM and arriving in CVG at about 6 AM, and in the opposite direction leaving CVG at 7:15 AM and arriving in LAS at 8:15 AM (all local time).
Alternatively, Delta runs 6 to 8 daily flights between CVG and Atlanta, and 9 or 10 daily flights between ATL and LAS.
So, if there is an issue with the direct flights, Delta has to send a different plane to service the route, or reallocate a different airframe that happens to be on the ground in LAS or CVG. On the routing through ATL, they can just rebook you onto the next flight, which will just be 2 hours later or so. Or, if the IRROPS occurs while you’re in ATL, Delta is pretty much guaranteed to have a spare airframe and crew that they can reallocate your flight to.
Just a point on the nomenclature.
Nonstop is just that. No stops.
A Direct flight is one that goes between cities, with one or more intermediate stops, but no change of planes.
A Connecting flight is just that. You change planes at an intermediate airport.
Connections are sometimes cheaper because of the inconvenience.
Most airlines employ a hub and spoke system. They choose one airport as a hub and have flights going to and from a bunch of cities.
I once took a flight from Amsterdam -> Atlanta -> JFK. The flight was with delta. Delta’s hub is in Atlanta. It’s cheaper (and logistically easier) for delta to bus a ton of people in and out of one city
Once an airline decides to fly a route, it costs very little for them to sell one more ticket. So when they have to, they’ll price it like that.
But, if they have a really popular route that people are willing to pay extra for the convenience, they want to price that as much as they can. And they do.
So, if you’re going from/to places that they already fly but are not as popular, they’d still rather sell you a ticket than not, even if it involves putting you on that more popular flight. You’re not getting on/off in the same place as the more expensive route, so they sell it to you for the normal cheaper price.
What everyone else is explaining about the hub and spoke system, and the reason your flight might involve a connection in the “wrong” direction is right, but I don’t think they answered your question about the pricing.
The airlines are pricing based on market value, not based on their costs. Would you rather take a direct flight, or a two-leg flight with a connection in the wrong direction? Obviously you’d rather have the direct flight right? Would you be willing to pay a premium to save some of your valuable time and take the direct flight? many people would, and that’s why those flights can command premium pricing compared to lengthier and less convenient multi-leg options.
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