Lots of variable costs outside fuel burn (They are becoming less of the equation though as fuel costs exceed 40% of cost):
Crew costs/duty
Taxi fuel
Ground Handling
Airframe Cycles
Engine cycles
Aircraft Utilization
ATC delays
Accidents/incidents (greater percentage in t.off/ldg phase). This is a stretch.
Variable revenue also:
If you can pick up and drop off passengers on the shorter segments, you'll generally get higher yields from the shorter distances. Adding to the bottom line of course.