Well in the last 8 years, such a thing would have been impossible, so that's hardly surprising.
As far as being unable to come up with a single reason, hunting is certainly a valid one (your experience hardly disproves the theory) as are collectors traveling to/from a gun show, someone moving/relocating, taking a firearm to be presented as a gift.
At the very root of it however, since keeping and bearing arms is a Constitutionally protected right, I don't have to come up with any reason to justify transporting a firearm on Amtrak - it's up to those who would want to prevent that to come up with a logical and compelling reason to infringe on that right.
My experience does not disprove the theorgy, but you are talking about one in over 2000 that might possibly take a train to a hunt. To reiterate, taking a train to go hunting is such a remote possibility that I don't know why one would need to use such a weak example for a reason to take a weapon on Amtrak. Same with taking a fire arm home from a gun show. Another weak example. So, those two removed, what other reason would there be for transporting a fire arm on Amtrak?
I agree that it is a Constituonally protected right and I am completely in agreement with that right. Yes, you are correct in that you don't have to justify transporting a firearm on Amtrak, but why would you want to?