Mata is set to start against Champions League opponents Steaua Bucharest.
Cech said: "I think that is his [Mourinho's] way of doing things.
"I don't know if Mata is being treated exactly the same as Joe but the manager has his own view on how he wants a player to play and it is up to the player if he meets the manager's expectation.
"If you play a great game and the manager thinks it's not exactly what he asked you to do, you can't argue with him because he's the boss. It's as simple as that. When you have a manager like that, you try to do what he wants.
"The manager is asking Juan to do slightly different things. As a player you have to make sure the manager is happy with you and have the right reaction to show that you deserve to be on the pitch. It was fantastic to see that Juan had the right reaction.
"He got his time at Swindon and again against Tottenham. He is doing his best and that's great to see."
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