From Megan McArdle,: auctioning landing slots
"Landing slots are a scarce public resource that are being overused because they're underpriced. "
This of course is true. Interestingly enough though, even airports with a monopoly airline (like say NWA at MSP) still have congestion problems, even though congestion is nominally internalized within the airline. In part this is because the delay is suffered by passengers as much as the airline itself (while airlines must pay more for fuel and salaries, the value of time of 150 passengers is pretty high, and not fully considered, especially when there is no competition).
An interesting series of papers by Joseph Daniel discusses this.
Daniel, Joseph I. Distributional Consequences of Pricing(1998). University of Delaware Economics WP No. 98-03.
Available at SSRN: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=106668
Daniel, Joseph I. and Pahwa, Munish, Comparison of Three Empirical Models of Pricing(1998). University of Delaware Economics WP No. 98-01.
Available at SSRN: http://ssrn.com/abstract=106648