Ronaldo appeared angry when he was withdrawn 19 minutes from time with United leading 2-0 as the Red Devils claimed their first league win in 2022.
Goals from Anthony Elanga, Mason Greenwood and Marcus Rashford took United to within two points of fourth-placed West Ham United.
"That is normal - a striker wants to score," Rangnick told BT Sport. "But he has come back from a little injury and it was important to remember we have got another game coming up.
"Also after what happened at Villa Park, we had to defend the lead this time and it was important that we went back to a back five and while we didn't keep the clean sheet, it was important to make sure nothing else happened."
Later in the post-match press conference, Rangnick added: "The only reaction I got was, 'why me? Why did you take me off?' I had to take the decision in the interest of the team and the club. We did the same thing when 2-0 up at Villa and didn't want to make the same mistake again.
"I understand Cristiano is ambitious but maybe when he is a manager in the future, he will make the same decision after 75 minutes.
"I didn't expect him to hug me after being substituted. I know how goalscoring players think and I had to make this decision. I have no issues with Cristiano. He was coming back from injury and hadn't played for one-and-a-half weeks. We had the likes of Rashford and Anthony Martial on the bench so why not use it? I would make the same decision again.
"I've been here now for six weeks and I've never had an issue with Cristiano. We had a discussion before the Villa cup game about his injury and we agreed not to use him.
"He was available again today and we decided to play him from the start. The most important thing is that we win games and this comes first."
