Flinders produced magnificent late saves to repel efforts from Dave McAllister and Luke Summerfield while Tom Bradshaw also struck the bar for the hosts as Pools claimed only a 13th point of their troubled season.
Hughes was impressed with Flinders but also frustrated his team did not push on once Charlie Wyke, a young striker on loan from Middlesbrough, equalised with a deflected shot in the 55th minute to cancel out a lead given to Shrewsbury by Jon Taylor midway through the first half.
"We were delighted to get the equaliser and were saying 'Come on, let's go on and win the game' but we seemed to get afraid," said Hughes. "There was a chance we might win and trepidation started to creep into our game and we started sitting too deep.
"We stopped expressing ourselves and at the end we've got Scott Flinders to thank for two wonderful saves in the last five minutes to keep us in the match.
"That's what he gets paid to do and he's come up trumps for us.
"In the dressing room afterwards everyone was saying well done to him but he still wasn't happy with his kicking. It shows you the perfectionist he is."
