The article covers this. The short answer though is price discrimination. Airlines want to sell tickets for the most total money they can. There is more demand for A-to-B tickets than for A-to-C tickets, so they are able to charge more. As long as selling A-to-C tickets is marginally profitable though, they will do that as well, even though the price is lower, and regardless of the fact that the most efficient way for them to move people from A-to-C is through B.
Basically airlines will charge what the market will bear; their costs on a given route don't really factor into it, except in as much as they won't generally fly routes that aren't profitable.
Basically airlines will charge what the market will bear; their costs on a given route don't really factor into it, except in as much as they won't generally fly routes that aren't profitable.