Their 3-2 derby success away to the relegation-threatened Iron was a 13th away win of the season for Rovers, who took full advantage of their title rivals' matches being postponed due to the snow and freezing weather conditions.
"We are quite comfortable with the position we are in," said Flynn. "You can see we have a group of players who work really hard for each other and that will stand us in good stead in the closing weeks of the season.
"I am delighted that our match managed to beat the winter weather and it could turn out to be an important weekend for us. I would certainly rather have the points on the board than have matches in hand. All we need to do now is try and keep the players relaxed and focused.
"What will it take to win promotion? More performances just like this. We are now learning how to see games out."
Doncaster got off to a flying start with an own goal from Scunthorpe defender David Mirfin after just five minutes. Iain Hume made it 2-0 after 39 minutes and although the Iron hit back through Mark Duffy two minutes later, a Chris Brown strike early in the second half sealed victory for Rovers.
A scrambled late reply from Karl Hawley was unable to prevent Scunthorpe from slipping to a 10th home defeat of the season.
Flynn added: "We know Scunthorpe are a team who come out of the blocks quickly, so it was important for us to start well.
"We had numerous good opportunities in front of goal that we did not take, and when that happens teams can come back at you.
"Scunthorpe would have got massive encouragement by their goal just before half-time, so it was important for us to start the second half well too - and we did with another early goal. But credit to Scunthorpe, they kept going well."