It will definitely take time, but if Sam is willing to give him time, he'll get used to it.

Yeah, yeah. Dean sees it. The way Sam takes time to answer Dean is good. It tells Dean that Sam has put thought into this, that Sam is thinking this, Ruby, through. Dean rubs the back of his neck when Sam says Dean wasn't there. He knows and he still feels guilty for leaving Sam alone, but at least Sam was alive; he'd taken care of his little brother the only way he'd known how. Dean won't apologize for making that deal. Dean gives Sam a bit of a sideways look. "She took care of you?"

He sounds doubtful because he is, but he's listening.