It is true that it's probably better for the President to travel by air - preferably landing at military bases. All air traffic shuts down around an airport before the President's plane is scheduled to land or take off. Roads and highways are also shut down for the Presidents motorcade. This is the reason the President often travels by helicopter - it's easier and more convenient to fly him from one location to another than it is to shut down all the roads.

It will be interesting to see what they do if he really wants to ride Amtrak. A private car is a must, even if it's a standard Amtrak car. They may have him board and get off at unscheduled locations where security can be tighter instead of a normal stop.