Billy Waters' first half strike proved to be the difference on yet another disappointing afternoon for the Saddlers.
Flynn explained Walsall 'went to pot' after the first goal and were guilty of sloppy passing and not carrying out the game plan.
He said: ''I have no problem with the fans' booing, if I'm honest I was doing the same in my head.
''We started brightly which was probably the only plus point, but after the first goal the next 20 minutes was up there with the worst performances of any of my teams.
''We have to lift ourselves now for Tuesday night which won't be easy but we will find out the character of the squad now.
"I will fight to the end there is no problem with my character and we owe the fans a response - I will be expecting one and so will they.''