Bobby isn't one for apologies for things after the fact. The best Ruby is ever going to get is that Bobby accepted the colt from her. Sam might have told her "baby steps" when it comes to his friends and family. If not, he will.

Sam can't fathom what Astaroth has done to her or encouraged Ruby to do. He might suggest that Ruby herself wouldn't know what details would weigh less on her until she actually does share them with someone. He would say that she doesn't have to open up to him if she's concerned he will treat her differently. He definitely only has vague notions of what Astaroth might have put them through had they not escaped. Some of those things Astaroth could have done could likely paint Sam as innocent as his wildest imagination is not malicious.

The safest option would be to get Ruby another car. She and Sam can talk about the method of how she acquires one later. He can't do much about her bare feet but help her adjust to put her feet up once in the backseat. He runs his hand through her hair quietly so she can rest from there.

Sam appreciates the silence until they've made enough distance between the motel and the road. He doesn't look up from Ruby even though he can feel Dean's eyes on him. He could reiterate that he hadn't thought it would have turned badly himself but he agreed he messed up. He had a gut feeling. Turns out, it wasn't wrong. "Yeah, uh, I realize that could have ended up much worse. Thanks for picking us up." He isn't making light of it, only keeping the conversation calm.