Lots of discussion in the Amtrak rider forums about this. Concerns from many folks about allergies, poop/pee, and the "Oh, my Fluffy/Fido wouldn't hurt anyone" pollyannas.
There's a 20-pound limit (pet and carrier), so it's not like we're going to see pit bulls, rottweilers and other large, potentially dangerous breeds. OTOH, in many years in dog rescue and other humane volunteering, the only times I've been bitten have been by the small, yappy ones. The big ones just want to lift their leg on my ankle.