The Rs went in at the break at Ewood Park 3-0 down and although a second-half brace from substitute Jamie Mackie gave them hope, it was ultimately too little too late.
The result left the London club above the Barclays Premier League relegation zone on goal difference alone and former Rovers boss Hughes - appointed as successor to the sacked Neil Warnock at Loftus Road last month - said: "I think it is still a case of getting to know what I have to work with.
"I have possibly seen things here that I didn't realise, so obviously I can work on that with them.
"We have got a break now for two weeks, which will help us.
"I will have a chance to work with the guys and then we have two home games which are vitally important to us.
"We need to be fully prepared and understand what it takes to win Premier League games - in the first half I don't think we ever understood what we needed to do."
Former Rovers boss Hughes moved to strengthen QPR's survival bid in the January transfer window by signing several new players, the most notable being strikers Djibril Cisse - currently serving a three-match suspension - and Bobby Zamora.
It was Mackie who made an impact, though, and Hughes saluted the efforts of the Scotland frontman, who had broken his leg at the same ground in an FA Cup tie last season.
"It was important for the boy," Hughes said.
"It was a bad time for him, but he has come through and been great - he has actually been unlucky not to be in the side.
"I thought when he came on that we needed his energy and willingness to try to affect the game and for him to try to get around people, and that is what he did.
"In my eyes, he has done his prospects no harm whatsoever. Maybe some of the other players, certainly in the first half, didn't do that - although in the second half, I can't really fault the effort, desire and belief to try to get something out of the game.
"You can't give yourself that much to do, though."
Blackburn looked set for a comfortable afternoon at the interval, with strikes from Ayegbeni Yakubu (15), Steven Nzonzi (23) and a Nedum Onuoha own-goal (45) putting them firmly in the driving seat.
Mackie netted in 71st minute and again in the closing stages to set up a nervy finale, but the hosts managed to hold on for the victory, the ideal response to last week's humiliating 7-1 defeat at Arsenal.
Rovers are up to 18th in the table, level on points with their opponents, and the return of top scorer Yakubu could prove vital to their prospects of beating the drop.
The Nigerian, who was in action again after a three-game ban of his own, now has 14 goals this season and it has emerged that QPR were keen to recruit him last month.
Blackburn manager Steve Kean said: "We had no bid from QPR for Yakubu, but I think there was always going to be plenty of interest - it wasn't only from QPR, there were many clubs that showed an interest.
"But when we said he was not for sale, it never got to the stage that there was any bid."
A Rovers player who was heavily linked with QPR in January is Christopher Samba, who submitted a transfer request.
It was rejected and he has not played since, but Kean insists he expects the defender, who has been nursing a hamstring problem, to be back in the team soon.
"He has had a clear scan - he had an MRI scan on his hamstring - which is good news," Kean said.
"I'm sure he will be back in full training early next week."