The 33-year-old defender did not wear the T-shirt in the warmup to Manchester United's Premier League game against Stoke City at Old Trafford, leading manager Sir Alex Ferguson to describe his action as "embarrassing".
"We will make sure Rio Ferdinand's rights as a human being, never mind as a footballer, aren't undermined in this," Carlisle told the BBC.
"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."