i have seen a dominican couple travelling on a metro bus with their dog, one of them little rat like chis. poor thing had to go in a luggage compartment under the bus, in a little transporter.
so i guess it can be done: just ask nicely and be super polite. however, travelling with suitcases, in bus's belly, alone in the dark (and heat), can be stressful for an animal so i suggest a rented car or a taxi. pay more but give your animals a decent ride.
ps if animals get car sick you can give them tiny amount of dramamine (sold here as dramanol).