A connecting flight will always be more convenient for some passengers, and there's no getting around that. However, there will be many passengers like me who prefer that a long haul journey only involve taking off and landing once, getting seated on a plane and queuing to disembark once, and the other necessary pains of air travel once, and at the more extreme end of things, domestic flights may have to be legislated against if the government finally realisies that the reason that there isn't sufficient capacity at our airports for economically beneficial international flights is the unnecessary domestic flights in their way.
And so with both things in mind, the railway certainly could do a lot more, for instance working to provide through booking and guaranteed connections, in order to gain even more custom from short haul domestic flights.
I don't think explicit legislation against domestic flights makes sense.
However, I do favor trips which take over 3 hours by train having roomettes available for maybe 10% less than the cost of a coach plane ticket, so that people won't take the plane to save money. Anytime fares are higher than that, it's evidence that Congress isn't spending enough money buying sleepers.
Maybe it makes sense to have legislation that says that airports that have parallel runways or are looking to have federal funding to get a parallel runway added need to have credible rail access in place before more airport expansion will be funded with federal dollars.
Then you get into the question of whath counts as adequate rail access. For Logan Airport, does the MBTA SL1 bus count? What about the shuttle bus that runs between the terminals and the MBTA Blue Line station? Those mass transit options are both imperfect to my mind, but I'm also not sure it's possible to do much better at any price tag. Even with an infinite track, tunnel, and bridge construction budget, I'm not sure Amtrak would ever really want to have its regular trains stop at Logan, because doing that would be a bit of a detour from other stations of interest.
Airports not remotely close to any rail service also bring up some interesting problems. On the other hand, I'm not sure I'd object to telling Phoenix that if they don't want rail, they don't get federal dollars with which to grow their airport.
There should be legislation to require that passengers arriving via a delayed train get the same treatment as a passenger arriving via a delayed flight by the carrier the passenger is transfering to, at least to the extent of not being charged to be put on the next available flight. Likewise, boarding Amtrak (or any other train operator directly serving an airport station that has reservations, but I don't think there are any) when transfering from a plane, Amtrak should accomodate passengers of delayed flights by letting them board the next available train at no additional charge. Maybe this should require buying the train and plane tickets on a single reservation.
Checked luggage transfers between Amtrak and the airlines may also be possible, except that there's so little checked luggage service on the NEC where most of the airports of interest are that maybe this wouldn't work too well. A guaranteed plane to Amtrak connection certainly ought to allow the passengers time to collect checked luggage from the airline.
Then again, if high speed service ends up requiring EMU trainsets to get good adhesion at a sane overall weight, and if crashworthiness ends up making a good argument for keeping revenue passengers out of the lead car, maybe there will be lots of space for checked luggage in the cab car on every high speed train.
Some of the Essential Air Service destinations strike me as much more cost effectively served by airplane than by rail, so I think that maintaining some domestic air service makes sense. I also think America ought to be a place that offers people choices, and if people want to sit in a coach airline seat going from Boston to LA in half the time the trip would take by a sleeper that goes over 200 MPH or faster track for just about the whole route badly enough to pay 10% more and some airline wants to offer them the service, I don't think we should stop them with legislation.
That's also an extremely good point. In the long term, lessening foreign energy dependence could be a tangible benefit to national security, and if there already were more electric trains and fewer flights, and more commuter rail and fewer cars, perhaps several wars already need never have been fought. Also, let's remember that Biofuels are part of the reason for disastrous rises in food prices, and will never be a substitute for tried and tested, reliable electricity-through-overhead-wires technology.
I'm not quite that pessimistic about the potential of biofuels. IIRC, the current generation of biofuels causing problems for food prices involve corn being converted to ethanol. Corn is probably overproduced in the US if we weren't trying to use it for more things than it should perhaps be used for, and there's a theoretical argument that animals raised to produce beef would be better off eating grass than corn. (On the other hand, I don't really like the taste of the grass fed beef I have eaten on a few occasions; then again, my favorite beef seems to be that which carries the organic label, and I don't think I've ever seen beef that's described as both organic and grass fed.)
This article suggests that algae may require less land area, and that the area of Maryland would be sufficient to grow enough biofuel for the US; I haven't figured out whether there's one Maryland of unused land in the US that can be provided with sufficient water to make this work, and I really don't know whether there would be any other major problems with doing that. If this would require massive amounts of chemical fertilizer and pesticide, there might end up being some environmental damage from that.
) want to suggest this? 
