Using Amtrack is no different than using pubicly funded roads to go to church or convention.
However... Suppose that a church or religious group of some size held a clearly non-secular event. They are expecting thousands. Should the city officials schedule extra busses or otherwise increase the availibility of transportation? It is their responsibility to provide public transportation. Is it reasonable to supprort, say a Star Trek convention, and not support say, a Billy Graham fest?
I would think that it would be their responsibility to provide the transportation and ignore the motivation of the citizens. Keeping tabs of the motives of the people is not their responisbility.
Following that line of reasoning then, I would think that it would be appropriate for public buildings to be used by any group as long as the criteria for use was the same for any and all groups who are interested. My basic faith in human nature leads me to believe that the implementation of this would be corrupted in no time, but the concept should be good.