But they might have been forgiven for believing that the fates were against them.
The loss of in-form striker Bobby Zamora was a blow midway through the first half and robbed them of their main attacking threat.
Faced with a Wolves side willing to go to desperate lengths to keep them out, they could have easily settled for feeling sorry for themselves.
But Hughes reorganised his forces and found a hero in Moussa Dembele, a £5m signing from Dutch club AZ Alkmaar, who scored an equaliser early in the second half and then grabbed the winner in stoppage-time.
Hughes said: 'Moussa was excellent and he's an exciting player. When he's in possession you expect something to happen and there are not many of his type in the Premier League.
'The longer he plays in this league the better he will get. When I had the opportunity to bring him over, I'm really pleased I was able to pull it off.'
Dembele's rescue act was no more than Fulham deserved from a bruising encounter in which Wolves had seven players booked and Christophe Berra sent off for a second bookable offence, which led to the 25-yard free-kick that clinched the points.
But referee Phil Dowd did not endear himself to the home fans by turning down two penalty claims which, with the benefit of TV replay, looked justified.
Berra, who had an eventful afternoon, appeared to trip Simon Davies in the penalty area in the seventh minute but was not penalised and, within three minutes, Wolves were ahead.
Kevin Doyle turned past Brede Hangeland and then delivered a cross to the far post which the unmarked Jelle Van Damme swept home.
When Zamora departed, the absence of a big target-man to battle against the no-nonsense centre backs of Wolverhampton appeared to be a serious handicap for the home side.
But Dembele, who started on the left wing, switched to a central role and showed his versatile talent.
Four minutes into the second half, the new signing displayed deft control to bring down a centre before stabbing a 15-yard shot past Marcus Hahnemann.
At the death, Berra committed one foul too many and was shown the red card and, from the resulting kick, Dembele shot through a hole in the Wolves wall.