England have been handed a seemingly straightforward draw for Euro 2016 in Group E along with Switzerland, Slovenia, Estonia, Lithuania and San Marino.
While Hodgson insists current England captain Steven Gerrard may still be involved, he views Rooney as potentially the man to take over.
Hodgson has no doubts that Rooney would have been focused on the World Cup even if he had not signed a new deal with United but is pleased the five-and-a-half year contract for the striker removes any uncertainty.
"I trust Wayne and even if his future hadn't been settled in this way he could have still focused on the World Cup," Hodgson said. "We're very happy for him and very happy for Manchester United and ourselves as well.
"Wayne, I'm sure, is a future captain of England because we are losing some of the famous players of the past who have served England so well. Steven Gerrard's playing magnificently for Liverpool and has been a major factor in their season so far, and I wouldn't want to write him off [for Euro 2016] but maybe when the day comes for Gerrard to hang up his boots, Wayne will be straight in there I'm sure."
Hogdson was delighted England have drawn Switzerland, the side he managed when they qualified for the 1994 World Cup and Euro 96.
"From an emotional, sentimental and nostalgic point of view, Switzerland was always something special," he added. "I was pleased to see them coming out of the hat even though they are having some success and are ranked high in the FIFA rankings."
Euro 2016 qualifiers will also see UEFA's 'week of football' idea put into action, with matches taking place every day from the Thursday to Tuesday of double-header international weeks. Hodgson, however, foresees some problems for England if they have to play an important game on the Thursday evening.
He said: "The major problem for us is that often before we get together with England, Sky Sports have their so-called Super Sunday matches often involving the best teams playing each other.
"If they are going to be playing on Sunday and we are playing on the Thursday then from a selfish point of view that is not going to be advantageous. But it's not all about what England want, it's what's best for other countries and I'm more than happy to go along with it."