Sure does. Landing fees, cost for refuling and extra time paid to crew for such a stop. What is the cost savings for those seats again? they send us emails on slide deployments costing $30,000, what do these fuel stops cost Tempe? Dare you publish the truth or stick your head in the sand like an Ostich?
A fuel stop can cost as much as an extra hour of time. If handling is last minute, extremely high fees are charged for last minute use of stairs, parking and any other facilities. Fuel, unless at a regular station, is high retail.
There are hidden costs also. At least one additional maintenance cycle is accrued and, likely, if any passengers are connecting overseas and miss their flights there will be those costs associated with accomodating them. Due to reduced frequency to the coast, recovery margins are becoming non-existent with negative implications not just from the DOT statistics but also the Star Alliance people start looking at how US "works" with the rest of the Alliance.
Marginally increasing revenue that increase costs is an exercise only a well-informed CPA is capable of, and for a gain of only a few dollars, would seem to hardly pay for the CPAs time.