And the Blues boss insisted the angry reaction of the travelling faithful was entirely justified after watching their side fall to a weak 1-0 loss at Whaddon Road.
Around 1,400 fans made the trip to Gloucestershire, only to see their team put in an insipid showing devoid of attacking quality.
The result means Pompey are now winless in five games - with just a single goal in that time.
Supporters made their feelings abundantly clear at what they’d witnessed on the full-time whistle, as the players and coaching staff applauded them.
And Cowley was clear they were well within their rights to do so.
He said: ‘It (the reaction of supporters) was fair. Absolutely, it’s fair.
‘We let them down and we know that.
‘We have to accept that, be big enough to shoulder that and take the deserved criticism which will come our way.
‘We have to accept we came up short and let a lot of people down.
‘It’s never a nice feeling, but it’s ultimately the truth.
‘We have to suck up the disappointment and respond to that.’
Cowley felt Pompey put in a reasonable first-half showing in which they’d got into good positions, before being let down by poor quality in the final third.
In the second-half, however, their shortcomings went much deeper in terms of the basic requirements needed to be competitive in games.
Cowley added: ‘For us, it’s always to fight, give your all and be honest.
‘For me that’s a really important quality.
‘They are the prerequisites before we even talk about quality - which we were really devoid of.
‘They are prerequisites - outwork, outrun, outfight.
‘I’ve been a manager 15 years and my teams have always been able to do that and when they don’t and come up short it hurts.
‘We’re professional people.
‘We give every minute of every hour of every day for this and this opportunity.
‘We know we’re in a very fortunate position and there will be millions and millions of people who’d love to be where we are.
‘So, absolutely, you go to the bitter end.
‘We were short really short of the prerequisites. That hurts me.
‘We’ll have to suck up that disappointment before getting back together again.’