Rooney's role as captain gives him "privileges" that the others don't enjoy said Van Gaal - including that he "shall always play."
The view of the Manchester United manager puts an interesting twist on his selection conundrum as he looks to juggle a raft of players who will expect to feature every week.
Radamel Falcao and Angel Di Maria arrived over the summer to compliment Rooney, Robin van Persie, Adnan Januzaj and James Wilson as options in attack.
If Van Gaal has his way, Cristiano Ronaldo could also be among his options in the future.
Juan Mata, who was signed last January, is one of the many options in midfield along with Daley Blind and Ander Herrera who joined over the summer as well. Antonio Valencia, Marouane Fellaini, Anderson, Ashley Young, Darren Fletcher and Michael Carrick will also be among those disappointed to miss out.
United started the season with a 3-4-1-2 system, but Van Gaal played 4-4-2 during the 4-0 win over QPR and his long-term aim is to get the team playing 4-3-3. Where everyone will fit is far from clear and Van Gaal is not making promises to any of them - except Rooney.
"Only the captain has more privileges," Van Gaal said.
"No other player has privileges.
"There are always players we put in the line-up in a team - my captain shall always play."
Manchester United 4 QPR 0 player ratings
Manchester United 4 QPR 0 player ratings
1/22 David de Gea
Was found wanting in the first half after very nearly being caught out by Matty Phillips. Did well to save from Armand Traore in the second period, however. 7
Posed a considerable threat throughout the match down the right flank and broke effectively. A good outlet for United. 7
3/22 Marcos Rojo
Slotted into the Manchester United backline with ease. Looked decent with the ball at his feet and showed a willingness to get forward. 7
4/22 Tyler Blackett
Perhaps a misfit on a teamsheet of Galacticos, the young defender didn't look out of place in Louis van Gaal's side. 7
5/22 Jonny Evans
Needed to be alert to a QPR counter attack in the first half but had precious little to do. 7
6/22 Angel Di Maria
Showed the ambition and ability to really trouble a poor QPR side at Old Trafford. His goal had an element of luck about it but his quality is undeniable. A man of the match display. 9
7/22 Daley Blind
Cut a composed figure at the heart of Manchester United's midfield and showed the Red Devils supporters exactly what they've been missing of late. 8
8/22 Ander Herrera
Took his goal really well and linked Manchester United's defensive midfielders up with the more attacking players brilliantly. 8
9/22 Wayne Rooney
Seems more mature with the captain's armband on. The England man put in another decent shift and grabbed himself an impressive goal too. 7
10/22 Robin van Persie
While the Dutchman always poses a considerable threat, he looks out of sorts at the moment. 6
11/22 Bets of the bench: Radamel Falcao
Didn't have long to make his mark but showed enough drive to enthuse the Old Trafford regulars. 7
12/22 Rob Green
Any goalkeeper who concedes four goals isn't going to score too highly. Made a number of decent saves which keeps his score respectable. 5
13/22 Mauricio Isla
Was brought to the club to give QPR a threat down the flank but continues to struggle in English football. 5
14/22 Steven Caulker
While the former Cardiff City man didn't do a great deal wrong, he went missing for large periods. 5
15/22 Rio Ferdinand
Would have had dreams last night of scoring the winner against his old club but was easily overrun by the new United talent. 5
16/22 Clint Hill
Taken off at half-time, his deflection took Angel di Maria's cross into his own net. A poor afternoon. 5
17/22 Junior Hoilett
Made little impact on the game but shouldn't let it get him down. These aren't the games which count for Rangers. 5
18/22 Niko Kranjcar
Showed glimpses of class but, like many of his team-mates, he failed to make his mark. 5
Didn't look match-fit at times and subsequently delivered a lukewarm performance on his debut. 5
20/22 Leroy Fer
Returned to the Premier League with QPR after relegation with Norwich City. Did little to suggest he will avoid that fate again. 5
21/22 Charlie Austin
A dangerous player at QPR's disposal but was left isolated for large periods. 6
22/22 Matty Phillips
Was bitterly unlucky not to score in the first half after David de Gea's error but it wasn't to be. 6
Van Persie, who is yet to score this season, could be the most vulnerable player in the squad because of Falcao's arrival.
Van Gaal denies having both players in his squad causes problems though.
"I don't think that Falcao interfered with Van Persie or Van Persie interfered with Falcao," the former Netherlands coach said.
"I think Falcao is a very good striker. I also said when he was coming in his first press conference that I like Van Persie also.
"Then we have Rooney and Januzaj and we have (James) Wilson. We have five players for the two striker positions and I have to choose."
Manchester United play Leicester City this weekend.
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