McIlroy is a huge United fan.
"If I was Wayne I would be very confused too," world No 2 two McIlroy said at his pre-tournament press conference ahead of the Open Championship at Muirfield.
"He's had nine great seasons at Man United and, reading between the lines of what's being said, I don't think he needs to prove himself to anyone.
"I don't think he needs to prove himself to the new manager. I don't think he should be playing second fiddle to Van Persie. He's been a great player and a very loyal player for Man United.
"If I was him I'd probably be in the same position. So I hope it gets sorted pretty quickly and he obviously stays at Old Trafford."
Asked if he had any advice for Rooney, McIlroy added: "He knows what he wants to do more than I... I guess he just wants to play football. I think he's that sort of player. He just wants to get on the pitch and show what he can do.
"And if he doesn't feel he can do that at United, he'll obviously want to go elsewhere. And I think that's very understandable."