The letter refers to moving people not freight (I think, I can't find it in the journal). The commuter trains weight is dominated by the rolling stock which has to be accelerated after each stop making it far less efficient than for freight.
I've done some quick calculations in the past and come to the same conclusions more or less. The CO2 emitted per person per mile by planes, fairly full light rail and efficient cars is remarkably similar. I guess this isn't too surprising since the total cost per mile (for people) is also similar. Carpooling makes driving fairly environmentally friendly compared to rail. By far the most green form of transport is a full bus, but that doesn't happen often, especially where I live in LA.
The bigger problem with planes is that this is all per mile and you can travel 8000 miles in a day - equivalent to most peoples years commute.