Peter Crouch had opened the scoring in the first half, tapping home from close-range after Peter Odemwingie's effort rebounded off the post, but Chico Flores equalised after 52 minutes when he headed Pablo Hernandez's cross past Asmir Begovic.
The result moved the Potters three points above of the relegation zone after a run of three games without defeat.
Strong winds made it a difficult test for both teams and Hughes admitted that a draw was probably a fair result considering the conditions.
"When you're the home side and you get your nose in front then you see the game through and you manage the game but credit to Swansea, they got on the ball and played like Swansea do," he told Sky Sports.
"They had plenty of possession. At times we allowed them to be a little bit too comfortable in possession but in the end, we're a little bit disappointed that we didn't get a penalty.
"There was two occasions, one when Pieters went through, I think he's been clipped and we all felt Bony had a handball in the area so you look at those things and think that maybe the game would've gone our way and we would've got the three points.
"In the end, we're happy enough with the one point. Asmir's had to make a couple of outstanding saves, we had one cleared off the line so all in all, we'll take the point today."
Hughes also praised Garry Monk's side as they limited Stoke to few opportunities, particularly in the second half.
"We, for whatever reason, didn't get on the ball as much as we have done this season," he said.
"Whether or not that was the conditions, but we were a little bit apprehensive in terms of getting on the ball the way we have done this year.
"You have to give the opposition credit in that. They closed us down quickly in key areas and didn't give us time to get our head up.
"All in all, we've come through the game. It wasn't a great performance by ourselves but we've got something from the game and we'll take that. Maybe a few weeks ago we wouldn't have been able to do that.
"Today was an opportunity for us we felt because with maximum points today we would have shown the league but we've had a decent return in the last three games so like I said, it wasn't a great performance but we got a point."