Some routes are literally subsidized - for example, the Essential Air Service program pays airlines to run flights to places that would otherwise be unprofitable to fly to, and due to the grants the airlines can offer the complete route for (relatively) cheap. So, for example, it might be expensive to fly New York to Chicago, but subsidized (and cheaper) to fly New York to Podunk via Chicago. But if lots of travelers catch wind of this, and pretend to go to Podunk only to get off at Chicago, then the air carrier doesn’t get their subsidy.