Charlie Adam's goal early in the second half was enough to separate the teams as the Canaries struggled to cause the home side too many problems in the final third.
Asked if his team deserved something from the game, Hughton told Sky Sports: "Certainly not a win. At half-time I thought we looked very good value against a Stoke team back to their most direct and we had to cope with that.
"I thought we coped with that very well during the first half. What we said at half-time was that if anything they were perhaps going to get even more direct in the second half to try and break us down and get that goal that they needed.
"We conceded at the worst possible time. We'd spoken about it and two minutes into the second half they've got the goal that they needed.
"Then you have to open up which we did in the end, changing our formation in the last half an hour, but we didn't do enough to win the game."