This hit home with me when I tried to buy a plane ticket to Chicago. I need to go there in mid-August for a meeting, and schedules dictate that I leave on Thursday and return on Sunday. Anyhow, I figured that one of the airlines that offers direct flights to Chicago from Tucson would be cheapest.
Nope. One direct-service airline wanted $374, but that required leaving Chicago very early in the morning. It was $447 if I wanted a return flight later in the day, which I did.
The other direct-service airline--allegedly a "low-cost" airline--wanted $479.60. Yikes.
I had non-direct options that were cheaper. The least inexpensive flight I found was a multiple-airline flight, available through one of the online travel sites. I'd get a direct flight to Chicago, but on the way back to Tucson, I'd have to fly through Atlanta--which any map will tell you is not really on the way. This would have more than doubled my in-air travel time on Sunday, so even though the ticket was a "mere" $309, I declined.
I ended up reserving a flight that requires a layover in Phoenix each way for $377. It only adds a couple of hours, tops, to my flight time each way, and it allows me to come and go when I want to.
So, my reservations are made, but these prices baffle me. We're in a world where longer, multi-leg flights on "regular" airlines cost a lot less than direct flights on "low-cost" airlines. Does anyone understand this?