I think the whole air\HSR comparison is very interesting, as far as capacity goes here is a somewhat unfair comparison:
-the busiest airport in the world, Hartfield-Jackson Atlanta Airport takes up 4600 acres and has 250,000 passengers per day
-the busiest train station (Not HSR) in the world is the Shinjuku Station in Tokyo, it takes up less than 15 acres or so and handles over 3.6 million passenger per day
(Maps are at the same scale)
Of course these passenger trips are different types but still that is a huge difference. If you compare the ratios for passengers per acre that is actually more than 2500 times more passengers per acre at the train station than the airport.
I would say that air travel is our best option for long haul trips (>500 mi), but that we can use HSR rail as both a competitor for short haul trips and a feeder system to bring passenger into airlines for long-haul trips. This would definitely be good to reduce the air traffic congestion at some airports.
I think stayinginformed gave a really good run down comparing of HSR and Air, I would say however that one study I read showed that the door-to-door travel times are actually pretty comparable in Europe comparing HSR and Airtravel for trips in the 190-250mi range, because there tends to be so much less "access and egress" time.
One of the big reasons people say HSR rail wont work in the US is because we dont have the density that Japan and Europe do. I wonder if that might be the exact reason we would want to build HSR, so that we could encourage high density land use and make urban living more attractive.
My only issue with it is how expensive it would be, they were projecting at least 50-60 Billion dollars for the CAHSR system last I read about it. But when it was on the CA ballot I voted absentee to fund it(the first 10 bil), their website says the 8 hour trip to my grandparents house by car that I have taken a hundred times would be just over 3 hours by HSR, that would be awesome!