City proved too strong for their Championship opponents as goals from Carlos Tevez, Gareth Barry and substitute Marcos Lopes helped Roberto Mancini's men into the fourth round.
Zola believes the game against the Premier League champions will prove to be a great learning curve for his young side.
The Italian was left to rue Fernando Forestieri's miss straight after City's opening goal when he went clear on goal, only to see Costel Pantilimon keep out his effort.
"What if yes, but what if does not exist in football," admitted Zola. "I was expecting something better than that, but I can't blame him for that.
"Normally Fernando is quite good in those situations, but the goalkeeper stood up quite well and it was a pity.
"I think the result was a little unfair to us. They deserved to win but not by that result."
Zola was happy with the performance of his young players, including goalkeeper Jonathan Bond, who made a number of impressive saves.
"He did very well and I told him not to be too disappointed, it was a very mature performance from a young player," added Zola.
"It is encouraging for all of us as we put a lot of faith in young players and it is a brilliant game for their education.
"I told them it would be impossible to stop them creating chances to score so they need to learn from better players if they want to become better players themselves and I am sure my players did learn a lot."