Robert Koren put Hull in front after 34 minutes before Billy Sharp levelled things up with his spot-kick in the 43rd minute.
Paul McShane won it for the Tigers with a close-range header after 69 minutes.
Agnew said: “I thought we were good value for the win. The shape of the team was good and we were resolute and tough throughout. We had what was needed to see the game out.
“We feel as though we should be competing at the top end of the division and where we are at the moment is very pleasing.
“What we have to do is find the consistency we would like to see over a period of time because when we have had a good run of results something has gone wrong.
“It would be nice if we could now take it on from this result and go through December remaining unbeaten.
“But we all know that in this league everyone seems capable of beating everyone else.”
Colchester will hand late fitness tests to Ryan Jackson and Brandon Comley prior to their clash with Yeovil.
Arsenal secured their place in the quarter-finals of the Europa League following their 3-1 defeat of AC Milan at the Emirates Stadium on Thursday.
Danny Welbeck scored twice against AC Milan to toast his England recall by sending Arsenal into the last eight of the Europa League.
Ipswich striker Joe Garner will not play again this season after it emerged he suffered a fractured skull against Sheffield United last week.