"There were some major decisions the referee didn't get right - he handled it very poorly," said the Rovers boss.
Hughes added: "He is one of the newer referees, that needs to be looked at."
The Cheshire official missed an apparent shove by El-Hadji Diouf on Fulham goalkeeper Mark Schwarzer that allowed Chris Samba to head into an empty net and put Rovers ahead.
Fulham later drew level through a Clint Dempsey header to preserve their unbeaten start to the season.
"Mark was clearly impeded in the build up to the goal. Diouf has no intention in going for the ball, he did it a few minutes previously and was again not punished," complained Hughes.
Hughes disputes Blackburn goal
"I don't think the referee has had a game like this before. You need experience to understand things that happen in and around the area."
Allardyce was similarly scathing of the young referee, who first officiated a Premier League game in February.
"Schwarzer handled the ball outside the area after seven minutes. That was the big major turning point. It possibly stopped Morten Gamst Pedersen's shot going in," fumed the Blackburn manager.
"Mark Hughes will say that Schwarzer was blocked for the first goal but he should not have been on the pitch at that stage. They should be down to 10 men."
The Rovers boss, who this week raised eyebrows when he claimed he was good enough to manage Real Madrid, was also unhappy about a series of other decisions by Taylor.
"Stephen Kelly's nutted El-Hadji in the back of the head and Carlos Salcido later pushed Mame Diouf in the back," he said.
"We've got four majors there - one went for us, three went against us. We feel that in the second half we should have two penalties."