Rovers' first-half performance was dreadful and they rarely managed to string a series of passes together before County midfielder Joss Labadie rocked them with a spectacular 25-yard shot which flew into the back of the net following a 14th-minute free-kick.
Flynn's side managed to raise their game slightly after the interval, but were unable to pinch an equaliser with Billy Paynter and Iain Hume having shots cleared off the goal line.
Flynn said: "The first half was probably the worst 45 minutes we have played since I took over.
"We tried hard to recover in the second half, but it didn't happen.
"We had a big crowd here and it was not an ideal way to end our home programme, but our fate is still in our own hands.
"I always thought it would go down to the final match at Brentford and I have stated that when I first took charge.
"We've dealt with being top of the table very well up to now - but not in this."
County boss Chris Kiwomya said he was proud of his players.
"We've got some young lads in the side and it was tough for them to come here against the leaders in front of a big home crowd," he said.