The Potters had the better of the chances against a visiting side that seemed worryingly laboured for large parts of the match.
Jon Walters was the most guilty, missing a wonderful headed chance from four yards after 15 minutes of the first half.
Hughes declared himself pleased with the result, however, and also spoke of his desires to allow his players to play in a more expansive style.
"I think the story of the game was that we were quite comfortable," Hughes told Sky Sports.
"We restricted [Manchester] City to bits and pieces in front of us but they never really penetrated us. I thought that when we were more progressive and upped our tempo we created some good opportunities.
"We just lacked that final ball or that appreciation of what was required at that key moment and weren't able to capitalise.
"As the season goes on we will continue to improve. I have a really strong group mentally and they really want to progress. Hopefully I can give them the platform to express themselves."