Hughes' men drew in their first-leg tie in Denmark as home substitute Martin Vingaard headed a stoppage time equaliser to mark his debut.
Nedum Onuoha had put City in front before Ailton pegged the Premier League team back prior to what looked set to be the winner from Stephen Ireland.
However, Vingaard's last-gasp equaliser ensured the honours were shared ahead of the return knockout meeting at Eastlands.
Hughes, though, believes his side are in the driving seat, saying: "We have allowed them back in right at the death and it is a little bit hard to take. We certainly had the chances to put the tie beyond Copenhagen.
Positive"But I think beforehand we would have taken a positive result with away goals. As it is we are still in good shape for the second leg and hopefully we will get the job done.
"I was really pleased with our attitude and anticipation of situations. We were a threat on the break."
Even though Robinho missed a gilt-edged chance with only a minute to go, Hughes was pleased with the Brazilian as well as Craig Bellamy and Shaun Wright-Phillips.
"They were the trigger for the level of performance we were able to produce," he added.
"Our front three, Robby, Craig and Shaun gave them a problem with their pace and ability on the ball."