http://cta.ornl.gov/data/chapter2.shtml
BTU per passenger mile can be approximated as follows (2002 data)
Amtrak 4830 Air 3703 Auto 3581
These numbers do include a load factor calculation, so if trains were larger and fuller or cars had fewer single occupant commuters, the numbers would change somewhat. It seems to me that airplanes are so close to capacity there is not much change available through increasing the load factor. Maybe the new generation of planes will have somewhat higher efficiencies.
By the way, intercity bus travel is included but not calculated in the table.
In summary, inter-city trains are not the most efficient way to travel today, using only a passenger mile per BTU calculation.
KGN