The former United defender believes the Bosman Ruling has fundamentally changed the emphasis in contract negotiations and left players with all the power.
His comments came at the end of an extraordinary week during which his former manager Sir Alex Ferguson lifted the lid on Rooney's desire to leave Old Trafford.
Bruce said: "That's the biggest part of all our jobs now. Tactics are only a little bit-part of what we face day in and day out.
"The biggest one is the man-management of the player now with the power they have since Bosman.
"The power is all with the players and that, for me, is sad because it is very, very difficult for any club, this just goes to prove, even Manchester United."
Bruce spent almost 10 years at United as Ferguson built a series of teams which took English football by the scruff of the neck.
But while he knows the game has changed markedly since he hung up his boots, he cannot accept Rooney questioning the club's ambition.
He said: "It just shows you, even the best manager in the world with arguably one of the best clubs in the world still has the problems we all face.
"It's not for me to question Wayne Rooney, but the only thing I find strange is, I played there for the best part of 10 years and to question their ambition, I find that unbelievable.
"I remember in '95 when Fergie sold Ince, Kanchelskis and Hughes, we all scratched our heads and thought, 'Wow, what's this?'.
"The introduction of Beckham and Scholes and the Nevilles and Butt produced a dynasty for 10, 15 years which hauled in trophy after trophy, so I would never, ever question their ambition, that's for certain.
"It's not often you get a player knocking on the door publicly to leave Manchester United.
"But there you go, even the biggest club and the best manager the world - as probably seen - has problems, so good luck Sir Alex."
Speculation is rife that 24-year-old Rooney will leave United in January with derby rivals Manchester City among those tipped to vie for his signature, and his departure could kick-start a flurry of transfer activity.
Asked if he would be interested in the England international, Bruce, with tongue firmly in cheek, replied: "We will make an inquiry to see if we can do a bit of back-up or a little bit of loan deal, maybe."
Sunderland already have one England striker on their books in the shape of Darren Bent.
The 26-year-old missed out on his country's Euro 2012 qualifier against Montenegro earlier this month because of a groin injury, but played for his club at Blackburn on Monday night despite missing 10 days' training.
Bent has now returned injured from international duty three times - he reported with a knock on one of those occasions - prompting Bruce to ask his medical staff to contact their England counterparts in a bid to get to the bottom of the problem.
Those discussions have now taken place, and it appears that the player has simply been unfortunate.
Bruce said: "I said to the medical guys, 'Can it be a coincidence that he has been there three times and come away three times injured when he has played here for 18 months and never missed a training session? Is there something we can try to solve and improve?'.
"The last thing England want is to injure him, and the last thing we want is for him to come back here injured.
"We have had a conversation through the medical people. There is nothing sinister in that, we just obviously asked if there is anything they are doing which puts Darren in danger.
"But no, he did it shooting and there is nothing in there that we can try to address."