Closest rivals Sheffield United suffered a heavy away defeat at Stevenage and Flynn said every point gained from now on was welcome.
"We can't rely on other teams," Flynn said. "We have to do it ourselves and make sure we stay on top until the end of the season.
"We didn't play as well as we can do - particularly in our passing going forward. The service to the front two wasn't good and our decision-making at times was not what it has been.
"When you are only a goal in front the other team is still in the game and you can't afford to give them any encouragement. But there will be ups and downs before the season is finished and the challenge is to stay positive."
Flynn refused to blame his side's performance on the bumpy pitch, but added: "Our away form has been scintillating. If we had matched it at home we would have been promoted already."
After dominating the match, Rovers finally made the breakthrough in the 37th minute when Chris Brown shook off his marker to convert a right-wing cross from David Cotterill. But the home side took their foot off the gas and Portsmouth cashed in when Jed Wallace fired home a left-footed shot from 10 yards after Patrick Agyemang had set up the chance.
Pompey manager Guy Whittingham said: "We are not too euphoric because it is a draw and not a win - whether we deserved to win is immaterial.
"Our results have been better recently, but it's been building for some time. Everyone knows the problems we've had with players coming and going, but the lads who are here now have worked really hard.
"The results we have been getting is a reward for that and it's very encouraging to see players with a spring in their step again."