The visitors more than held their own against title-chasing City, but were undone 20 minutes from time when Yaya Toure found a way past Asmir Begovic.
Hughes was happy with his side's performance, but disappointed not to see their efforts rewarded after putting so much into the game.
The Stoke manager felt a couple of errors in the lead up to City's goal prevented his side earning a priceless point.
"In terms of the performance we were relatively pleased because I thought certainly in the first half we were organised and restricted them to very few opportunities and had good opportunities ourselves," he told Sky Sports.
"Joe Hart made an outstanding save to stop Charlie Adam from scoring so we had a number of similar situations. From our point of view we were a little bit disappointed we were taken out by Man City players when good situations could have developed.
"But in the second half you know City are going to come out and up the ante. We had to batten down the hatches and repel the pressure without really looking in too much danger, to be perfectly honest.
"But the one lapse where we made a couple of consecutive errors, we didn't win the tackle on edge of the box and allowed the cross into the box, and we didn't track Toure as he came in to get on the end of things. Consecutive errors more often than not lead to goals.
"Overall we were still very much in the game, still pressing and in the end I think City were happy with the 1-0 result."
Hughes believes Stoke can take positives from their two displays against City as they prepare to face Arsenal next weekend.
"We've played City twice this year and only conceded one goal home and away, so that shows we are resolute and have a group of players that are committed to what we are doing. We can make it difficult for any team in this league and Man City, I believe, are the most accomplished team in the league this year.
"We have been able to cause them problems and restrict them to very few chances in two games and we have another big game against Arsenal next week and we will have to do much more of the same."