The 21-year-old defender has enjoyed an extended run in the side after making just two appearances for the Reds during the last campaign.
Rodgers believes that the full-back is now reaping the rewards of working hard on the training pitch.
"We're seeing a different young player from when Jon came into the team," he told the club's official website.
"I now see a young player around the training ground that looks full of confidence and has got the belief now that he belongs in the squad. It's a wonderful testament to his character."
Flanagan scored his first goal for Liverpool last month during their 5-0 win at Tottenham Hotspur in the Premier League.