Why is the direct flight to LA more expensive than the flight to San Jose with a stop in LA? You'd think the price for the San Jose flight would be the price of the LA flight plus the price of the LA to San Jose flight.
They will pay extra landing fees, burn more fuel, fly further, and have one more cycle on their very costly engines to bring you from A to B, so by all metrics, it should be more expensive.
But hey, people are "willing" to pay more for the direct flight, so why not charge them as much as they can, while suing the skiplaggers for "costing" them money..
Similar reason I can get a flight from London to Rome for £20, yet Sydney to Queenstown is a minimum of $300.