The 21-year-old was overlooked by both Roy Hodgson and Gareth Southgate for the national sides' upcoming fixtures, with the senior team in action against Denmark and the Under-21s facing Wales.
But Rodgers is surprised at the rationale behind the decision, especially as Flanagan's appearance in the 3-0 win against Southampton was his 15th for the Reds this season.
The Liverpool boss was especially puzzled by the absence of Flanagan's name on the Under-21 squad list, with Rodgers of the opinion that the full-back could easily have earned a place in Hodgson's senior squad.
"I couldn't believe he wasn't even in the U21s!" the 41-year-old told reporters after Liverpool's win over the Saints.
"I thought he might have been in with a chance of the full national team because he's played in big games since he came into the team and has been outstanding - but I was equally as surprised he wasn't in the U21s.
"He is a young player and still has a way to go. He's improving all the time - you can see home and away he's playing at a really high level.
"He'll just continue to improve and develop and I'm sure he will get in there at some stage."
In the same press conference, Rodgers also paid homage to the tactical flexibility of the Liverpool squad, with the Reds having used a variety of formations during the current campaign.
"We've played 4-3-3, 4-2-3-1 and 3-5-2 and today we played a 4-4-2 diamond," he said.
"You've got to heap huge praise onto the players, who kept the tactical discipline in order to block up the space and be a threat going forward.
"Our players were tactically brilliant today; kept a clean sheet collectively as a team and scored three goals."
Do you think Flanagan deserved an England call-up?