Rooney has signed a new five-year contract after previously indicating that he wanted to leave Old Trafford.
But Aston Villa boss Houllier admits contracts "do not mean a lot" since the advent of the Bosman ruling.
He cites the example of Cristiano Ronaldo, who was under contract but left Old Trafford for Real Madrid in the summer of 2009.
Ex-Liverpool boss Houllier said: "I don't know what happened really (with Rooney). I was impressed by Sir Alex's press conference because he responded well to the situation.
"It was not easy and he felt emotion which showed the liking he had about the player.
"I think in the end I would say, all (sides) win because I wouldn't imagine Rooney outside of Manchester United.
"I like the boy, I like the manager, it is a good club, and he probably made the right decision regarding contracts.
"But you never know what happens. Ronaldo had a contract as well and he left and when a player wants to leave maybe you can delay that for one or two years.
"It is not good when a player has nine or 10 clubs and this is why I think Rooney has taken the right decision in his development, whatever happens next year. We don't know.
"Whether Wayne has realised he can't play for Manchester City, I don't know."
As regards player power in football, Houllier added: "The power came with Bosman. But now it comes even one year before the end of a contract and the new FIFA rules.
"That is why the contract does not mean a lot. This is why at some stage we need to think about the future because you know teams that succeed have got a certain type of stability.
"What Chelsea are doing is interesting because they won the double but look at the team and how long they have played together.
"You see the team now and they are gradually improving and to get stability and to improve the level of your football, you need a bit more protection."