We frequently travel with our dog. We have had good experiences in Hilton hotel brands, particularly Hampton Inn and Home2Suites. They do charge pet fees. You also have to check each hotel individually because they all have different requirements for weight and number of dogs, even within the same brand.
Our dog has a cushioned bed on the backseat and seems pretty comfortable there. We stop every couple hours and take turns in the bathroom and walking her around. We have a couple collapsible bowls and pour water into one at each rest stop so she can drink. It’s really not so hard.