Goals from Nacho Monreal and Alex Iwobi were enough to propel Arsenal to a 2-0 triumph at the Emirates.
Albion came close on a couple of occasions, though, with Solly March striking a post in the first half and substitute Glenn Murray glancing a header against the side-netting late on.
Despite the defeat, Hughton believes his team can leave with their heads held high.
He said: "When you come here you know it is going to be a difficult afternoon. They've got such quality, you have to set your team up and make decisions on how you want to start things.
"When you are promoted team, as we are, it makes it even more trickier but I certainly felt there were more positives than negatives. You have to remain concentrated for the whole 90 minutes here, we just needed to make more of the good areas that we'd got ourselves in to."
Albion stay 14th in the table - with seven points from as many matches - heading in to the second international break of the season.
It's a start that has satisfied Brighton boss Hughton. He added: "I don't think you are ever over satisfied and there are a couple of games we felt we could have got more from. There's slight disappointment because maybe we could be in a better position. What we have done is shown in games, especially against Manchester City and Arsenal, that we are able to compete."