Rovers broke the deadlock after an evenly-contested first half-hour when Iain Hume struck in the 35th minute after shaking off a couple of defenders to fire home from the edge of the box. Despite their efforts Hartlepool never really tested home goalkeeper Gary Woods, although substitute Steve Howard was unlucky to head against the post in the 77th minute.
By then Rovers were 2-0 up after James Coppinger had fired home in the 55th minute after latching on to a left-wing cross from teenager James Husband, who then produced another superb delivery for Billy Paynter to head in the third nine minutes from time.
Flynn said: "We needed to be at our best against a team that had been playing well and are fighting for their lives. They made it difficult for us at the start and we needed something out of the ordinary to break the deadlock.
"Iain Hume provided that for us with a super goal when he showed great technique to finish with a bit of style. I was pleased with a lot of aspects of our game, especially keeping a clean sheet and with the way we quickened up the pace and were very professional in the second half.
"You have to enjoy yourself when you are top of the table and we look as if we are playing with a smile on our faces. Why we've got where we are is because the team comes first. There were some great individual performances, but it was the collective effort and display that was pleasing."
Hartlepool manager John Hughes handed credit to Doncaster afterwards and agreed they were worthy winners.
"Sometimes when it's not happening for you that's when you have to do something to turn the tide, but we were unable to do that," the Scot said. "We weren't able to reproduce the standard we have set recently, but we need to be consistent to have a chance of staying up.
"We are fighting for our lives, but I think we tried to play a bit too much football and never really landed a glove on them, which was disappointing. We were second best, that's for sure, but we've given ourselves a chance with the run we've had and we've got to get back on song for the next game on Tuesday night.
"The games can't come quick enough for me at the moment and I'm looking forward to the next one to put things right."