Paddy Madden put the home side in front and they had a handful of chances to kill the game - while Walsall's created next to nothing all game.
That was until the 89th minute when Andy Williams glanced home a Danny Cashman corner to rescue a point in front of the 1,250 strong travelling Saddlers fans.
The result still leaves Walsall without a win in 12 games - but Flynn hopes the late goal can help turn things around despite his side's below par display.
He said: "They kept going all the way.
"It was a poor performance, but we have played better and not got any points so it is something for us to build on at least.
"I hope it gives us a boost but I have just said to them, I don't think we could have played any worse today if we tried, it was painful to watch if I am honest.
"But we kept going, we looked the fitter team at the end and we got a point.
"I am not going to get carried away but at least we have something to build on."
During the second half the away fans made their feelings about the display and the run the Saddlers were on with a series of chants.
And they sarcastically cheered when Walsall had a shot on target - and the Saddlers boss admitted he understands the frustrations but paid tribute to them for travelling in their numbers.
"They want to see their team do well, and so do we, we want to do well," said Flynn.
"It was a fantastic turnout, over 1,200 here and at least they will have something to half smile about and be happy about on the coach home, but the performance needs to be better.
"Not many times has the performance not been there, the result yes, but the performance has generally been good."
Walsall had Williams to thank for rescuing a point as he came off the bench to notch his first goal in Saddlers colours.
And Flynn believes it will be a weight off his mind now.
He added: "I'm pleased for Andy, nobody works harder than him he is a first class pro and is always first in and last out.
"So it'll be a good weight off his mind to get his first goal and get a point.
"Now we have two tough home games and we need to start winning."