Rooney appeared set to move away from Old Trafford when it emerged last week that he had refused a contract offer from United.
He released a statement expressing concern about the "future squad" and the "continued ability of the club to attract the top players in the world", but went on to sign a five-year deal after negotiations resumed.
Ronaldo's departure from United to Real Madrid in 2009 brought in an £80million fee but saw the club lose a key asset, and Chelsea went on to win the domestic league and FA Cup double as Sir Alex Ferguson's side had to make do with a Carling Cup victory.
Madrid were one of the clubs linked with a possible move for Rooney had his relationship with United disintegrated to the point where it could not be repaired.
However, Ronaldo thinks Rooney is at the ideal club.
Ronaldo said on Sky Sports News: "Rooney knows what's best for his career so we have to respect his decisions.
"I think the best club for him is in Manchester, of course."