Rangers went into the international break rooted to the foot of the Barclays Premier League, having taken just two points from their opening seven games, and some fans have called for manager Hughes to be sacked and replaced with former Tottenham boss Harry Redknapp.
But Fernandes told talkSPORT on Monday: "We just have to be patient, I have full faith in Mark and the team and the coaching staff."
He added: "Of course, we need a couple of results. But we have to be real.
"You could be Sir Matt Busby, Sir Alex Ferguson, or whoever the greatest manager is.
"But when you're suddenly playing with four centre-backs and you haven't had the stability of a defence - every game he's had to change, put people out of position - we're going to struggle a bit."
Fernandes became majority shareholder just over a year ago at QPR, who sacked manager Neil Warnock in January.
"We've only been around for one year," he said. "Rome can't be built in a day and I'm not a short-term person, and we need stability more than anything."
Asked about the increasing demand for the club to send an SOS to former Tottenham boss Redknapp, Fernandes said: "Many people have told me that I should lead the board.
"When you go down to Loftus Road, fans there are very reasonable and they understand what we're trying to build and I don't think anyone wants an unstable situation."
Source: PA
Source: PA