The 21-year-old lost his position as City's first choice goalkeeper after the arrival of Shay Given from Newcastle for £6million in January.
To compound his misery the former Shrewsbury shot-stopper has also lost his place in Fabio Capello's England squad, after failing to earn a call-up for the latest get together ahead of games against Slovakia and Ukraine.
But Hughes is backing his charge to bounce back from the disappointment and in the future establish himself as No.1 for both club and country.
"It is important Joe knows our feelings with regard to his ability," the former Blackburn boss said.
"Joe is going to be England's outstanding goalkeeper for the next 10 or 15 years.
"But it is right that we have been able to take him out of the fire, allow him to step back and see where he is.
"It is different with outfield players, because you can keep taking them out and putting them back in again.
Scarred"You can't do that with a goalkeeper, and there are too many examples of young lads who have ended up burnt and scarred and never recovered.
"I don't want that to happen with Joe."
The Welshman indicates that he was always on the lookout for an experienced keeper this season and admits that he would even consider sending Hart out on loan next term to ensure he continues his improvement.
"I said at the outset we needed an experienced goalkeeper," he insisted.
"I made an offer for Brad Friedel, and even though in the end nothing happened, I still felt we needed more experience because Joe was bound to suffer fluctuations in form.
"The opportunity with Shay presented itself, and when that happens you have to move.
"Initially Joe found it very difficult. But he has got his head down now and knows he has to work.
"We can then look at him going out on loan next year, because we want them to develop, and maybe just training day after day is not what they need.
"It is something we will definitely investigate, while always keeping in mind we want them as players for Manchester City."