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 equalizer with Billy Paynter and Iain Hume having shots cleared off the goalline.
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. A few of the players were edgy and not their usual selves, but I've no doubt will be up for it in the last match.
"Our away form has been blistering and we won't go there lacking confidence.
"We were beaten by a super strike at the end of the day. The fans tried to lift us and we had a go at the finish but, if I'm honest, I'm not sure whether we deserved a draw."