On another day the Us could have scored several goals but in the end they were frustrated by some below-par finishing.
It was Scunthorpe who carved out the best two scoring opportunities of the afternoon. Both of them fell to striker Hooper, one in either half, and on both counts he fluffed in front of goal.
He was clean through in the first half, only to completely miss his kick with just the goalkeeper Jimmy Walker to beat.
In the second half, he dragged a shot wide in another one-on-one situation.
The Iron were mostly content to soak up the pressure and defend in numbers.
Scott Vernon squandered Colchester's best chance of the first half when he failed to connect cleanly with an empty goal beckoning, while the Us' main dangerman Mark Yeates warmed the hands of keeper Joe Murphy with a couple of long-range thunderbolts.
Colchester almost secured all three points in the last minute of normal time.
Man-of-the-match Dean Hammond, who played a fine captain's role in midfield, sent substitute Steven Gillespie through on goal with a superb throughball.
Gillespie, who has just returned from a hamstring injury, hit his shot well enough but it rolled agonisingly wide of the far post.
Colchester have won only two games at home since they moved to their new Community Stadium, from 12 starts.
It is their away record that is keeping them away from the relegation zone, but on this display it will only be a matter of time before their home form clicks into place.