The Blues were too good for the Potters and went through thanks to Oscar's superb first-half free-kick following a foul on the edge of the box.
"Overall Chelsea on the day deserve to go through, but I was pleased we were very much in the game right till the end," Hughes said.
"It was a fantastic strike (by Oscar), but we were a little bit disappointed with the initial award of the free-kick; we felt it was a challenge that didn't merit a free-kick. There was very little contact.
"But you have to hold your hands up when a player produces a little bit of quality like Oscar did.
"You have to get a little bit of luck when you come to places like Stamford Bridge and maybe we didn't force the issue enough to change things in our direction.
"You're never happy to go out of a cup competition, but in terms of performance I'm reasonably pleased."
Stoke play Sunderland on Wednesday and could have Peter Odemwingie in the squad, with Hughes expecting a swap deal which will see Kenwyne Jones go to Cardiff to be completed on Monday.