The 29-year-old has failed to score in United's first two Premier League fixtures of the season and looked off the pace in Friday's 1-0 victory against Aston Villa.
Following the departure of Robin van Persie earlier this summer, Rooney looks set to remain the focal point of United's attack and Van Gaal is adamant that the England captain will flourish.
"All the media has written for one year that I have to put him in the striker's position so it's amazing that, after two games, you're doubting your own opinions. I cannot understand that," Van Gaal told reporters.
"I have always confidence in my players."
Adnan Januzaj scored the winner at Villa Park in his first appearance of the new campaign and Van Gaal has urged the 20-year-old, who started only seven Premier League games last season, to show consistency this term.
"He [had] to compete with 24 players last year and he is 20 years old," said the United boss.
"The characteristics of a young player is that he's not consistent and he has to show that this season.
"It's possible but, at a club like United, you never have a guarantee of a position in the top XI. Every player here knows that, and because of that we have a very good team spirit."