Winkelman's club face the League Two side in the FA Cup second round on Sunday, the first time the two teams have met since the London club were relocated 60 miles north to Buckinghamshire in 2003.
The hugely controversial move outraged fans of the club, and Winkelman concedes it was a "crass" decision, but he is pleased with the current state of his League One team.
He told the London Evening Standard: "I don't think I will ever be accepted by AFC.
"I now accept it was probably pretty crass to go and do it the way I did. I wasn't so involved in football that I understood all the nuances.
"My actions over the last eight years, none of them are pariah-like. We run a really good football club."