Hodgson made six changes for the final Group B clash against Slovakia, including a rest for his captain in midfield, and saw his side held to a goalless draw.
That result left them second behind Wales, with Hodgson heavily criticised in some quarters for changing the team before the job was done.
A meeting with Iceland in Nice on Monday is not the most daunting of punishments but there have been reports that some Football Association board members looked upon the tactic unfavourably.
Rooney himself appeared less than happy as he passed Hodgson at full-time, having come on as a second-half substitute, but insists he backs the manager’s judgement.
“I think it’s a decision we had to make in terms of keeping players fresh for the knockout stages,” he said.
“I respect Roy’s decision to play me or rest me. He’s the manager, it’s his decision, not my decision, and I have to respect that.
“As a player you want to play, of course, but in terms of me now going into the game on Monday I’ll be a lot fresher.
“It’s a great chance for the players who had the rest to use the energy we gained from not playing the 90 minutes and I’m sure that’ll be good for us in the later stages of the tournament.
“He had a tough call with what he had to do and he decided to leave six players out from the previous game.”
While England will be heavy favourites to see off Iceland, the smallest nation ever to reach a major finals, the remainder of their potential route looks decidedly tricky.
Hosts France await in the quarter-final should they manage to see off the Republic of Ireland, with one of Spain, Italy or Germany likely to emerge in the last four.
But Rooney believes plotting a possible route to the final is a fool’s errand. He said: “I’ve seen a lot words saying that England will have to beat Iceland then France, Spain...whoever.
“But who says they are going to go through? Who says we are?
“This tournament has already thrown up a lot of surprises. If we’re to go further we’re going to have to beat some very good teams.”