"I'm incensed, it was a genuine attempt to get across the guy, no intent whatsoever," the Rovers boss told Sky Sports after the 1-1 draw at Ewood Park.
"We tried to get the assistant to change his mind but he decided to send him off.
"It has taken the edge off the game for Tugay.
"Everybody was very disappointed he was sent off because you want to see people like him play."
Jermain Defoe equalised for the visitors from the resulting spot-kick but moments later Mido appeared to handle the ball in his own area but referee Phil Dowd waved away protests from the Rovers players for a penalty.
"Mido clearly handballed soon afterwards and these are big decisions," Hughes added.
"This is three or four occasions this season when referees have not got these big decisions right.
"It's a game we should have won comfortably.
"We were by far the most strong and powerful team and, with an even wicket, we would have won comfortably.
"Mr Dowd did not have the best of games to say the least. I'm sure he would admit he has had a shocker."