Benitez was appointed as the replacement for Carlo Ancelotti in June following the Italian's dismissal in May - a year after he guided Real to their 10th Champions League title.
Zidane, who won a league title and scored the decisive goal in the Champions League final in 2002, worked as Ancelotti's assistant for a year before moving to his current role as coach of the reserves.
And Fernandez, who enjoyed managerial stints at Athletic Bilbao, Espanyol and Real Betis and is currently in charge Guinea's national side, was disappointed by the decision to part company with Ancelotti, but feels Madrid are preparing to eventually hand the reins to Zidane.
"I would have preferred Carlo to stay," Fernandez told Omnisport. "The season before last, Madrid won the 10th Champions League. They were competing against a great Barcelona team, a great Lionel Messi.
"I was disappointed that he left the club. I would have liked him to stay at the club.
"Benitez doesn't have the same style. They prepare everything for Zizou, who I think will be the next Real Madrid coach."