This is one of the dumbest ideas I have ever heard of, unless, as the OP suggested, it were a sep car... Like this idea I posed on that pet-board a few minutes ago........
Dog, cats, pets of ANY kind on public transportation, (other than short jaunts of subway, etc) is a BAD, and STOOPID idea....
I am a pet lover, and have had dogs, cats, (and ALL the "little critters" that come when you raise kids ) my entire life.
The LAST thing I want to do however, is to pay for a room (or a seat) that was just moments before occupied by a traveler, who "just loved her little 'Pookie', and let the dog/cat out of the crate, to crawl all over the roomette........"
Forget about the occasional ****, poop, or vomit that WILL happen if pet travel were allowed on trains.
And "segregate" those who are allergic to pets, and those who aren't? ("...like they do for smokers.........") sorry ain't gonna work. Not enuff equipment NOW on Amtrak, and why should Amtrak have to incur all the additional cleaning, sanitizing, etc ., etc., that would HAVE to happen
Best idea would be some entity to purchase, and staff baggage/pet cars that are environmentally safe for pets, and put them on Amtrak in lieu of the regular baggage cars. (thereby freeing up some much needed rolling stock)
Then if you want "little Pookie" to travel with you on the train, put the Pookie" in their cage, and charge them a super-premium to cover the costs of the new baggage/pet cars, and staff.
Dogs are dogs. Cats are cats. They are animals. Leave at home with someone to watch them, or kennel them. They won't die. They won't even probably miss you that much.
My daughter treats her two toy poodles like they were children, makes ME wanna vomit.