Stoke won 1-0 thanks to Charlie Adam's early goal.
Hughton said: "Today we were up against a Stoke side at their most direct and most physical.
"But you know what you are going to get when you come here, and I don't have too many complaints. It's something you have to deal with.
"I thought, if anything, they would get even more direct in the second half and we would have our chances.
"But to concede so early in the second half really hurt us, and with this defeat it means we've still work to do.
"We've two home games, which is a plus, and the situation is still in our hands."