Gunners boss Wenger had accused Rovers of using "violent" tactics during Sunday's 1-1 draw at Ewood Park but opposite number Hughes believes the statistics prove Blackburn were the better side in every way.
Hughes said: "I was delighted with the way we played and I was disappointed with some of the comments after the game which I did not believe were warranted.
"We dominated a good Arsenal side and that has been borne out by the ProZone statistics that show in every facet we were better than Arsenal and we even outpassed them, which is the first time that has happened against them.
"But I am not going to dwell on it too much because I know how well we played."
Hughes was backed up by defender Stephen Warnock, who said Blackburn were aggressive but also played good football.
The full-back said: "I think there are a lot of lads like me who like to get stuck in and I think that's why we are such a good team.
"We are a physical team but if you look at the stats we are a team that likes to pass the ball as well.
"That gets taken away from us a lot of the time and Arsenal can say what they want but you never see them bringing those stats out when people want to put us down."