The Cheshire official missed an obvious shove by El Hadji Diouf on goalkeeper Mark Schwarzer which allowed Chris Samba to head into an empty net.
Rovers boss Sam Allardyce was also critical of Taylor - claiming Schwarzer should not even have still been on the pitch because of a "blatant" handball outside the box.
Hughes said: "It was a foul for their goal so we are disappointed and our performance in the second half merited a win.
"I don't think the referee has had a game like this before, it's only his second game in the Premier League.
"I just feel there's a lot going on off the ball when you play the likes of Blackburn and you need an experienced referee to recognise that and understand what's going on.
"Maybe that's why he missed the challenge on Mark.
"I was disappointed with the award of the goal, there were two other incidents prior to that so for the referee to allow the play to continue was disappointing."
Clint Dempsey headed home expertly as Fulham brushed off a poor first half display to finish on top and maintain their unbeaten start to the season.
Hughes added: "In the first half we allowed ourselves to get a little bit penned in and didn't really play our own game.
"Blackburn will always put the ball into the box and make it difficult for you.
"I wanted us to get the ball down, move it quickly and play our game rather than Blackburn's, and we did so and scored a great equaliser.
"It was another away point and we are still unbeaten so we are pleased."
Allardyce admitted that Diouf had committed a foul but claimed that Schwarzer should have been sent off earlier for handling Morten Gamst Pedersen's chip outside the area.
"We have got away with that perhaps but we were exposing Mark Schwarzer's weaknesses and he handled outside the box blatantly.
"The referee's in a fantastic position to see and he should be sending him off and he doesn't.
"We've exposed one of their weaknesses in that the keeper's not great on balls into the box."
Allardyce insisted that Rovers should also have been awarded two penalties for challenges on both Dioufs - El Hadji and Mame Biram.
He added: "On 67 minutes Kelly headbutts Diouf and 999 times out of 1,000 if it's outside the box he blows up for a free-kick and a dangerous challenge and probably books him.
"We had control of the game and it was disappointing in the second half we got edgy, lost our rhythm and let Fulham back into it.
"Our quality wasn't good enough and I'm quite satisfied on the basis that we got a draw when most of the time this year I have been disappointed in the result and not the performance."