Rhett says that Bonnie is the first person who belongs wholly to him, whereas Scarlett doesn’t—this is because emotionally, Scarlett “belongs” to Ashley, whom she loves. For this reason, Rhett is able to freely express his love for his baby daughter in a way that he can’t for Scarlett. This makes him more sympathetic to people like Mammy, but Scarlett starts to speak of him like she spoke of Charles and Frank: in feminine-coded, unflattering terms. Naming Bonnie after the “Bonnie Blue flag” is also a nod to the past, as they’re referring to a flag associated with the Confederacy.