More than 30 players from eight Premier League clubs chose not to support the annual Kick It Out campaign over the weekend by refusing to wear a T-shirt.
Among them was QPR defender Anton Ferdinand, who was racially abused by Chelsea captain John Terry last season.
Hughes said: "It's very difficult to eradicate totally. Let's hope that will happen but we will be a lot greyer."
Ferdinand was joined by team-mates Djibril Cisse, Shaun Wright-Phillips, Nedum Onouha and Junior Hoilett in making his protest at the perceived lack of action about racism during the warm-up before Sunday's 1-1 draw Everton - three visiting players, Victor Anichebe, Sylvain Distin and Steven Pienaar also chose not to wear the T-shirts."My understanding at the beginning of the week was that everyone was going to comply," said Hughes.
"But a lot of people have made stands and possibly some of our guys felt that they needed to stand shoulder to shoulder which I think you have to accept.
"Any campaign that looks to address an ill in our game and in society needs to be supported irrespective of the fact of whether they are doing enough or not.
"[Some] players feel it's time to make a stand and try and affect the authorities in terms of what they're doing and if it does that and they are better in fighting racism in sport then it's a good thing."
Source: QPR MAD
Source: FOOTYMAD
