Yaya Toure opened the scoring for Manchester City early on, before a superb Bobby Zamora strike levelled things for the London club after the break.
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"Their second goal was a real body blow because we'd worked so hard to get back into the game," Hughes told reporters. "But I was really encouraged by what we produced in the second half.
"You could see we were trying to get the ball down and we've got good players.
"Once we've had a number of games together and once we've had more experience of playing with each other as a team, there's no doubt we'll get better.
"They [Man City] understood they were under a little bit of pressure and there was a little bit of unrest in the stadium. There was a little bit of nervousness about their play and we tried to play on that.
"All in all there are a lot of positives. We can look back on that and think we've got something to build on.
"We had a number of chances, but unfortunately from our point of view, they fell to the wrong guy in Ryan Nelsen.
"On another day, they might have fallen to one of our strikers, but all in all, we're moving in the right direction."