It was a horrible day for the Tykes, who started the day clear of the drop zone but now find themselves once again in the bottom three after Peterborough and Huddersfield picked up victories.
Seven wins from their last eight at Oakwell had galvanised the South Yorkshire club, but with matches against promotion-chasing Hull, Nottingham Forest as well as a final day clash with relegation rivals Huddersfield to come, the outlook is looking more bleak.
Flitcroft however sees things differently.
"Today will end and tomorrow will begin - I'm looking forward to tomorrow and galvanising a group of players that are hurting," he said.
"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."
Flitcroft was keen to praise Charlton's attacking talents but admitted he tried to counter their early strikes too aggressively.
"I think the two strikers (Ricardo Fuller and Yann Kermogant), they were excellent," he said. "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."