The Portugal star was forced to miss the clash on Saturday as the furore surrounding his red card against Athletic Bilbao at the start of February continues.
Ronaldo was sent off after he clashed with Carlos Gurpegi in the 1-1 draw at San Mames, with Real twice appealing the subsequent three-match ban.
The second attempt was rejected by the Spanish Sport Ministry's Administrative Court just a few hours before Saturday's clash, as Real were once again forced to make do without their talisman.
Ancelotti was still content with how his side performed in what ended up being a routine win, although he could not hide his frustration at being without Ronaldo.
He said: "I'm satisfied because we demonstrated that we are solid. We could have played better but I'm happy.
"Nobody was happy that Ronaldo couldn't play. It wasn't normal that he was suspended for three matches.
"We played well and won without Cristiano, but I still can't understand why he got suspended."
Ancelotti was impressed with the individual performances of numerous players, hailing goalscorer Gareth Bale as "brilliant".
The Italian added: "Bale's performance was good before the goal and brilliant after it.
"(Asier) Illarramendi had a great game. He is becoming more confident. I'm very happy for him.
"Raphael (Varane) had a good game too. He didn't make any mistakes. (But) Alvaro (Morata) is thinking too much about scoring. He needs to focus on playing well instead."
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