Rovers, who will now be without striker Chris Brown for a minimum of four weeks due to a knee ligament injury, missed out on top spot for the first time this season - with Bournemouth's win over Crewe on Tuesday night taking them to the League One summit.
"It was obviously an opportunity missed to go top but we eradicated some of the problems we showed on Saturday," said Flynn, referring to Doncaster's 2-1 defeat at home to Walsall.
"It was a high-octane game with a lot of physical challenges and chances at both ends.
"We had a game plan and we stuck to it and it was important we made some amends for the last two games.
"It's important not to lose a home game and it will prove to be a valuable point."
Rovers' best chance at the Keepmoat fell to striker Billy Paynter just before the break but he shot over from eight yards.
"He tried to hit it too hard," said Flynn.
Izale McLeod missed a couple of good chances for the Dons, for whom Daniel Powell also tested impressive Doncaster goalkeeper Gary Woods.
"He made some fantastic saves, important ones as well," added Flynn.