Anton Ferdinand, whom John Terry was found guilty of racially abusing by the FA, as well as Djibril Cisse, Alejandro Faurlin, Junior Hoilett, Nedum Onuoha and Shaun Wright-Phillips all opted not to wear the shirts in support of the anti-racism group prior to their 1-1 draw with Everton.
While Sir Alex Ferguson claimed that he could file disciplinary action against Rio Ferdinand for declining to wear the shirt on Saturday, Hughes is adamant that he won't come down hard on any of his players.
"There was a discussion between the players at the beginning of the week," said Hughes. "My understanding was that everybody was going to wear the T-shirts.
"It's a personal thing but my belief is that any campaign trying to take racism out of football and sport is a good thing and we should all try to support it. Everybody will have their own view on that. Some will say they are doing enough, some will say they aren't doing enough.
"I think the strides the English leagues have made in the last 20 years have been excellent. When I started playing football it was a hell of a lot worse than it is now. I realise we should never be complacent. The point has been made that players want more to be done. I am sure because of the strength of feeling, people in these organisations will question themselves and maybe that's good. Maybe that's why the guys feel strongly enough to do that."
QPR travel to Arsenal in their next Premier League game on Saturday.