A fine goal from Leon Best just before half-time settled the game in Newcastle's favour at St James' Park as the Magpies moved into sixth place in the Premier League.
For Hughes it marked a losing start to his reign, having replaced Neil Warnock this week, but the former Fulham and Manchester City boss took some positives from his side's performance and felt they deserved to get something out of the game.
He said of his players on Sky Sports News: "I was pleased with their application, they gave me everything they had, obviously we've been done with a little bit of individual skill in our own box.
"In terms of our play I think we created a number of reasonable chances and on another day those will go in for us. It would have been ideal obviously if we could have got something out of the game because overall I felt we deserved something.
"It's a hard place to come, we understand that, it was never going to be easy so that's why I'm encouraged by what I saw today."
He added: "We haven't had that much opportunity to work on our attacking play, it was more this week about making sure our shape was good and everybody knew what was expected of them and I think you could see that in our play.
"We were nice and solid, and everyone was working in relation to one another and that augurs well for the future and I think the longer we have the opportunity to work with the guys and given their application today, they'll only improve."
Regarding the possibility of adding new faces to his squad during the January transfer window, Hughes added: "If there's quality available and attainable then we'll pursue that but they have to be the right players and they have to be the players who can come in and make a major impact because otherwise there's no point bringing them."
Asked about Blackburn defender Christopher Samba, Hughes added: "It's common knowledge we've put in a bid for Chris Samba. We have a number of players we would like to bring to the club. We'll have to wait and see."
Newcastle manager Alan Pardew praised his side for their discipline in protecting their one-goal lead.
"We were disciplined with the goal that we had and tried to look for another. And then in the last period of the game we were just seeing it out really, it was a nice disciplined performance from us," he said.