Victor Anichebe, Sylvain Distin, Steven Pienaar
Anton Ferdinand, Djibril Cisse, Shaun Wright-Phillips, Nedum Onouha and Junior Hoilett
Micah Richards, Joleon Lescott
Hughes said: "It's very difficult to eradicate totally. Let's hope that will happen but we will be a lot greyer."
Ferdinand made his protest at the perceived lack of action against racism during the warm-up before Sunday's 1-1 draw Everton.
He was joined by team-mates Djibril Cisse, Shaun Wright-Phillips, Nedum Onouha and Junior Hoilett, while three Everton 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. If it does that and they are better in fighting racism in sport, then it's a good thing."
Rio Ferdinand will be dealt with, says Sir Alex Ferguson
Everton manager David Moyes backed his trio of players, but conceded he did not necessarily agree with their decision not to wear the T-shirts.
"I spoke to the players and they decided it was their decision," Moyes said.
"I listened to their reasons and I told them my reasons why I thought they should, but ultimately it's one of these things. They have to make that decision."
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