Several Premier League players, including Ferdinand's brother, Rio, refused to take part in the campaign that was led by Reading striker Jason Roberts and the Manchester United man could be disciplined by Manchester United boss Sir Alex Ferguson as a result.
And, although Hughes was under the impression that all his players would participate, he understands why the defender, who was racially abused by John Terry during a game last October, chose not to.
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"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."
The Hoops boss reaffirmed his support of the work being done by Kick It Out but warned that the fight against racism will not be easily won.
"It's very difficult to eradicate [racism] totally. Let's hope that will happen but we will be a lot greyer," Hughes added.
"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."