Stephen Dawson and Thomas Kennedy were sent off during a nightmare 90 minutes at Oakwell which ended with Flitcroft's side in the bottom three and a point shy of safety.
But the defiant manager said: "Today will end and tomorrow will begin - I'm looking forward to galvanising a group of players that are hurting.
"We will have two players missing (through suspension, it's about regrouping a gang of players who do want to play in this league.
"That will have emotionally scarred some players, but it hasn't scarred me. We can move on from this."
On the game he said: "I think the two Charlton strikers (Riccardo Fuller and Yann Kermogant) were excellent. As a partnership it was probably the toughest we have faced, we didn't deal with it.
"I might have gone chasing the game too soon, that is something I will take away. There were too many holes, we were not solid enough and we have paid the price."