The Metropolitan Police is formally looking into claims Chelsea's Terry abused QPR's Ferdinand in October.
Fernandes told BBC Sport: "I think innocent until proven guilty.
"There's been no hard evidence either way of John's alleged statements. If he's the right man for the job, then he should be selected as captain."
BBC Sport understands that Terry, 30, has been included in Fabio Capello's preliminary England squad for November's friendlies against world champions Spain and Sweden.
In an interview with the BBC, Fernandes added that he agreed with the comments of former England player Paul Ince, who said that Terry is not necessarily a racist even if the allegations against him are proven.Chelsea lost 1-0 to Premier League rivals QPR and had two players sent off
"Lots of things can be said in the spur of the moment which don't make you really believe what you've said," said Fernandes.
"I don't think you can write someone off as a racist because of one statement. Having said that, it is in the public eye and people like John have to be gooder than good. If he said it, it is wrong because of who he is but I don't say he's a racist because of that one statement."
The Football Association (FA) is also looking into the alleged incident, which relates to Chelsea's 1-0 loss at Loftus Road on 23 October.
Blues captain Terry has denied the allegations, while QPR defender Ferdinand, 26, has given a statement to the FA, adding that he has "very strong" feelings on the matter.
Ferdinand declined to elaborate further until a "thorough" FA inquiry has been concluded.
The FA announced it was conducting an investigation after it was alleged Terry shouted racial abuse during the west London derby.
Some viewers also claimed video replays from the match showed Terry using racist language.
Terry was stripped of the England captaincy in February 2010 following allegations he had an affair with the ex-girlfriend of Wayne Bridge, an international team-mate.
Terry was reinstated by Capello in March after the Italian deemed a year without the armband to have been sufficient "punishment".For the latest updates throughout the day follow Sportsday Live. Have your say on Twitter using the hashtag #bbcsportsday