The Yellow Submarine were reduced to 10 men in the second period of the 1-1 draw when Gabriel Paulista was sent from the field, with Bilbao forward Aritz Aduriz levelling late on after Tomas Pina had opened the scoring.
"I won't talk about referees because when they are talked about, they're ridiculed," he told reporters at a press conference.
"The referee's performance was lovely... I thought we had a democracy here where you could say what you wanted. We were in control of the match before the sending-off. We were the better side.
"In the 180 minutes we've played against Athletic, we've had 10 men for 75 of them. Their goal was predictable. They are the favourites to get into the Champions League."
Villarreal currently sit sixth in La Liga, while Bilbao sit fourth.