Stokes was cleared of the charge, which he denied, at Bristol Crown Court last month and was able to play a part in England's series victory over India after missing the second Test.
However, Flintoff believes it will take the 27-year-old time to regain his best form after the traumatic experience of appearing in court.
Speaking on his BBC Radio 5 Live podcast, Flintoff, Savage and the Ping Pong Guy in a discussion about sporting comebacks following Tiger Woods' first PGA Tour victory for more than five years, he said: "Do you know when someone comes back and they lose a little bit of their aura and you gotta find it? Ben Stokes.
"Ben Stokes goes through what he's come back from and to me, I watch him play and it's not the same Ben Stokes...at the minute. To me, there's a bit of an unsureness about him.
"You're aware of what people are thinking and that does rub off on you. You're not just trying to win a game, you're trying to win people over.
"He's doing all right, but it's not that Ben Stokes that we saw pre- his trial. And it takes a while to come back from, and I hope he does."