Why are connecting flights more expensive than nonstops?

Q: Whenever I book a flight on US Airways and look at the list of flights, the cheapest flights are the nonstop flights.  The flights that go through connecting airports are dramatically more expensive.  I just booked a round trip from Atlanta to Charlotte for $87.  One of the flight options that went through a connecting airport was $1,000 one way.  Why would someone pay that much to fly through another city, particularly when the turn around time might only be half an hour?

A: That $1000 fare was probably a glitch of some kind. On longer haul flights, nonstops are almost always more expensive than connecting flights. But perhaps on shorter routes that an airline flies nonstop, such as US Air flying between Charlotte and Atlanta, their reservation system isn't set up to calcuate cheap connecting flights. You'll find, as stated above, that on a Charlotte to, say, Los Angeles, which US Air does fly nonstop, they're charging $365 RT right now; but Northwest is  offering connecting flights for $177 RT.