Aircraft are more efficient at cruise altidude. The more time spent at 36,000 feet and the less time spent taking off and landing the cheaper the overall flight is. Stage length is a critical factor in profitability. The same aircraft that flies once for 16,000 miles might make 2-3 3,000 mile flights in that same time. That's 2-3 more take offs and landings, 2-3 more landing fees, 2-3 more maintenance walk arounds etc... The numbers add up.