I see two potential advantages for high speed rail, over air travel, especially as it relates to trips of less than 300 miles. One has to do with the fact that rail is already inherently more "green" than air. And going forward, rail offers up a more realistic opportunity for taking advantage of future advances in green alternatives, than does air.
And second - especially on those shorter trips, rail can save us considerable otherwise wasted time. Realistically, from the time we set foot in an airport to the time we leave the airport - subtracting out actual flight time - we spend at least 2 hours (figured very conservatively). This is true of virtually any flight of any length and it's unrealistic to expect that we can do much to reduce that. So, IF we can create a rail system with a "hop on / hop off" regime, the time savings would be enormous and worth $Zillions.
As it stands now, I doubt that either of these cost factors is being considered in these cost comparisons between rail and air.