Ten Hag saw his team huff and puff to no avail against relegation favorites Burnley at home to Sunday.
The Dutchman was booed by home fans for his decision to substitute Rasmus Hojlund and Kobbie Mainoo.
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Speaking in his post match press conference, he said: "I am the manager and have to decide what the team needs.
"It was the right decision and totally logical to bring off very young players who are in their first year of the Premier League and feel some fatigue.
"They have both had injuries this season and I want to protect them."
He then added: "Fans need patience.
"I understand they want to see the skills of these players but the league gets more intense year by year and the youngsters need to adjust. That takes time."