The Potters, who are winless in the Premier League this season, lost the third-round game to an injury-time strike from Markus Henriksen.
After the game, Hughes said: "We have just gone through 90 minutes of a totally dominant performance, really.
"In the first half I think we started really intense, causing Hull a lot of problems, and we scored a great opening goal, a fantastic strike from Marko.
"Then (Hull scored) with probably their only attack of the first half - you have to say it is a fantastic finish.
"We're scratching our heads at that point, wondering how we are going in at half-time on level terms, but we came out in the second half with exactly the same intent and were continually asking questions of Hull, who looked content to just to soak pressure up and get through to penalties, it seemed.
"So to lose it right at the end is a little bit hard to take, I have to say, because I think the performance merited a win.
"We were the side that were trying to make things happen and creating chances, but unfortunately it didn't lead to us progressing in the competition, which is what we wanted."