Per-passenger subsidies on flights (many of which average 3 passengers or less) are greater than the subsidies to Amtrak. In most cases, passengers just drive to larger airports for non-stop flights, but airline and airport lobbying keeps the waste alive.
Alex cites a USA Today piece noting a just-approved subsidy for Atlantic Southeast Airlines (a Delta regional affiliate and the single worst airline operating in the continental United States) to pay
60% of ASA’s cost to fly two round-trips a day between Macon, Ga., and Atlanta’s Hartsfield-Jackson International Airport, 81 miles away. The airline projects that passengers will pay an average of $78 for a one-way ticket – and that flights, typically on planes with fewer than 70 seats, will run 83% empty.
I suppose it could be worse: the same funds could be put to use enhancing security theatre.
Update: Evan Sparks has much more (including graphs!).