Marc Pugh struck the game's only goal in the second half, but Barnsley's display before the interval in particular belied their status as Sky Bet Championship strugglers and they were unlucky not to head into the break with a one-goal lead as Chris O'Grady and then Steve Dawson both rattled the same post in the same move.
Barnsley continued to create chances throughout the 90 minutes and only a fine block denied substitute Jason Scotland a late leveller.
"I told the players to give it everything and they have done," Flitcroft said. "They put everything I asked of them into a football match and it wasn't good enough to get anything out of the game.
"Certainly in the first half I was delighted with the way we played and in the second half they got on top of us and we couldn't stop them at times.
"We still had chances; the two that hit the post in the first half and on another night they go in and we comfortably win the game.
"I can't ask anything more from that group of players - they work hard for each other and give it everything.
"We came here to win the game and I've thrown everyone on and gone really positive. I've told the lads after the game to keep working hard."