The Professional Footballers Association chairman criticised the brothers in his recent book for failing to support the anti-racism T-shirt demonstration and failing to explain their stance at the time.
Carlisle wrote in the book that he was "bitterly disappointed" with the boycott, which saw players - including the Ferdinand brothers, Manchester City's Joleon Lescott and Reading striker Jason Roberts - refuse to wear T-shirts issued by Kick It Out before a round of Premier League fixtures last October.
He went on to label the players, exempting Roberts, as "s***houses" for not explaining their reasons.
But he told Sky Sports News that those comments reflected his emotions at the time of the boycott, and he has since talked with the players and understands their position.
"The danger of serialisation of the book was that they are my personal opinions at that moment in time," he said.
"So when the whole Kick It Out boycott kicked off, that weekend I did not understand what was going on. I did not agree with what was happening and I voiced that in all the interviews I did.
"My frustrations were at the fact that nothing was forthcoming from the group of players that boycotted the T-shirts.
"But as you read the rest of the book, [you can see] the issue evolved and we talked about what they were bringing to the fore and the reasons why they did that. I did then come to understand.
"I respect them for using the platform that they had to raise their umbrage with Kick It Out and how racism was being tackled."
The Football Association have introduced a minimum five-game ban for being found guilty of racism, while FIFA and UEFA have signalled their intentions to follow with similar minimum suspensions.
Carlisle welcomed the moves but still feels there is not enough being done.
"It is a step in the right direction," he said. "But personally I still don't feel it is anywhere near enough."