The Potters fell behind in the first half through Jonny Howson's long-range strike and never threatened an equaliser as they slipped to their first home defeat of the campaign, but were left aggrieved as Kenwyne Jones was pulled back by Leroy Fer in the penalty area in the second half.
Stoke are 8/1 with bet365 to beat Fulham 1-0
"We were below par today," Hughes told reporters after the match.
"This is a Premier League game and we need players to perform and we haven't.
"It's only today that they have let themselves down, it was a disappointing performance and we were poor. We never got any pace or power into our game which is unlike us.
"If the referee sees it, he will agree there is an infringement, Kenwyne Jones was trying to get on the end of the ball, the letter of the law says it should be a penalty.
"But we needed to be better today but they were comfortable when they got the goal and overall we were well below it."