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 Jim Coppinger had fired home in the 55th minute after latching on to a left-wing cross from teenager James Husband, whoroduced another superb cross 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.
"Every game is difficult in this division and there will be one or two setbacks before the end of the season, but if we continue to play like this we will be alright."