After Saturday's 4-2 win, the Scot insisted Ferdinand had let the club down and would be "dealt with".
While PFA chief executive Gordon Taylor felt the protests were "misguided", Carlisle, who works as an ambassador for Kick It Out, confirmed that the PFA will support Ferdinand in this instance, though he is keen for players to continue their backing for the campaign.
York City defender Carlisle added: "Everyone has a right to free speech. Just like you can't coerce anyone into shaking hands, you can't make somebody wear a T-shirt, although I do personally believe that joining in with the campaign is the best way forward.
"There are two sides to this one. First of all, Sir Alex Ferguson is continual in his unwavering support for the Kick It Out campaign, which is commendable, but you can't vilify or coerce any individual for making a stand.
"I would sincerely hope that Ferguson now speaks with Rio Ferdinand, asks him why he wanted to make that stand and hopefully supports the position he is in and it isn't seen as a player-against-manager situation."
The former Manchester United defender told MUTV: "I don't agree with Rio. I don't see where he is coming from and I don't know what it is going to achieve."
Anton Ferdinand was one of eight players who chose not to wear Kick It Out T-shirts ahead of QPR's Premier League clash with Everton at Loftus Road on Sunday.
The 27-year-old defender was joined in his protest by Rangers team-mates Shaun Wright-Phillips, Nedum Onouha, Djibril Cisse and Junior Hoilett. Everton's Victor Anichebe, Sylvain Distin and Steven Pienaar did not wear the T-shirt either.
PFA boss Taylor told TalkSPORT he was disappointed that the players took such a decision.
"I feel to some extent it's misguided and I feel it's quite disrespectful of people like Herman Ouseley, who has spent a lifetime fighting racism," he said. "I can understand the frustration but the fact is Kick It Out is not the disciplinary body."
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