Defender Jamie McCombe scored the only goal of the game for Rovers in the 80th minute, but the Robins barely tested home goalkeeper Gary Woods.
Flynn said: "I thought we controlled the game and our keeper didn't really have a lot to do.
"It was a good performance and a very important victory and I'm pleased for the players and the fans.
"We are five points clear at the top before the rest of the teams play and I'm not really bothered about who is behind us so long as they stay there.
"We should have had a couple of penalties and won by more goals but thankfully it didn't matter in the end.
"The timing of the performance and the result was perfect after losing at Coventry on Friday.
"It was important to bounce back after a defeat and that's all down to the character we have in the dressing room.
"We are all focused on getting Doncaster back into the Championship."