Despite a promising performance from the visitors, in which Robert Huth twice had headers cleared off the line and two penalty appeals were turned down, Darren Bent's late winner broke Stoke's hearts.
Hughes' charges had opportunities to score through Stephen Ireland, Huth and Marko Arnautovic throughout the game as they dominated for much of the game.
Whilst Hughes was understandably unhappy with the result, he was impressed with a marked improvement in his side, who disappointingly lost at home to Norwich last time out.
"As the away side, I thought we took the game to Fulham," Hughes told Sky Sports.
"Early in the second half we were very much in control and looked the team more likely to score.
"Unfortunately we had a misplaced pass in a poor area and created something which I believe was their only shot on goal.
"In terms of the game itself I think we were the more dominant side, which is encouraging in terms of away performances.
"We're desperately disappointed and upset we haven't been able to get anything out of the game. The minimum requirement was at least a draw.
"It's hard to take, and Fulham will count themselves lucky."
The aforementioned two penalty claims will stick in the minds of Stoke fans, with first Stephen Ireland and then Jonathan Walters both appearing to be felled in the penalty area in the first half on separate occasions.
Former Fulham boss Hughes shared similar misgivings over the decision, pointing the finger at the linesmen and match referee Roger East.
He said: "I think they're good claims. If they'd have been given when they occurred it would have changed the outcome of the game.
"They're the big decisions that you want the officials to get right. In my opinion they didn't."
Hughes did reserve praise for new boys Ireland and Arnautovic, however, who impressed as attacking threats at Craven Cottage.
"They did well. They probably tired towards the end but it was encouraging for us."
After three successive defeats in the Premier League, Hughes would be forgiven for panicking with his side floating above the relegation zone after seven games.
The Welshman still sees the positives though, and expects his side to kick on soon and pick up crucial points.
He said: "We have to look at playing well away from home, and at some point in time we need to start taking opportunities.
"I was more concerned last week. Today I thought we played okay, as well as against Arsenal. We're getting better each time.
Hughes left Fulham in 2011 citing a "lack of ambition" at the club, but was happy with the reaction he was given by the home fans.
"The reception was fine. I didn't hear a great deal until they scored. There are a lot of good people here."