Well, the difference is that Rhaenerys was actually in the line of succession, for Cersei to even be considered she would have to be of Targaryen or Baratheon descent or related by blood to King Robert.
So it would be like this Robert-Joffrey-Tommen-Stannis-Renly-Myrcella-Shireen-False Aegon (if proven to be a Targ)-Viserys-Daenerys- False Aegon if he's a Blackfyre- Prince Doran on the basis of being descendant in some form of house Targaryen-Arianne-Quentyn-Trystayne-Oberyn and Monterys Velaryon, by the law of succession Cersei wouldn't be anywhere near it.
Cersei wasn't ruling officially, Tommen was. She was just suggesting things he can do, and temporary regents could be appointed if the king in question is considered too young, that's what Robert wanted Ned to do. Be the temporary Regent until Joffrey came of age, and thus that is what Cersei is doing with Tommen (unofficially) but she would not be able to hold court or sit in the throne even if the Dance of The Dragons had never happened and the line of succession wasn't patrilineal, she simply doesn't have the lineage.
So no, Rhaeneyra actually held court, she ruled (for a little while) through her own and not through her children, she was IN the line of succession.