My Emma is a spoiled one, who gets to travel all the time. Anytime I have off two days in a row (I work retail, so that only happens once or twice a month now), my fiance, Emma, and I hop into the car and off we go.
Red Roof Inns and Motel 6's (both Accor hotels) will always take pets, so long as it's not prohibited by local law. With Red Roof Emma has managed to go up and down the eastern seaboard a few times now. We even got lucky with a Red Roof just one block from the beach (dog friendly on-leash, mind you) in Myrtle Beach- and the room even had a jacuzzi!
It's not nearly as hard as one would think to travel with your babies.