The Newport County boss felt the Exiles’ 2-1 defeat against the Blues came to a side destined for League One.
But he felt his team would have snared a point with another five minutes on the clock at Fratton Park.
Pompey were 2-0 up and cruising against Flynn’s men with goals from Kyle Bennett and Kal Naismith.
But Alex Samuel made it a nervy final 14 minutes as he pulled a goal back for his side.
Flynn explained he felt his team’s opponents will enjoy success this season.
But he knows his outfit gave the Blues a fright.
Flynn told the South Wales Argus: ‘This is a very good Portsmouth team and I’m certain they’ll go up this season.
‘But Cookie was full of compliments. He thought we’d given them a right scare and he couldn’t wait for the final whistle.
‘The boys did themselves proud, they kept going and that’s all I can ask of them.
‘It’s a difficult position that we’re in but they are fighting and we’ll carry on fighting.’
Flynn was disappointed with how slow his side were to start against Pompey.
He also thought the referee denied County a first-half spot-kick.
He said: ‘Let’s be honest, we didn’t start playing until we went 2-0 down.
‘We had a clear-cut penalty that we should have had in the first half.
The boys were convinced it was a penalty and when you come to places like Fratton Park you need that bit of luck.
‘I was disappointed with the goals we conceded but again the effort was there from the lads and we finished strong.
‘I think if there was another five or 10 minutes in the game we would have got the draw.
‘We had three big chances at the end and we should have taken one of them but the boys kept going and they were outstanding in the end.’
– JORDAN CROSS