The Potters fell to their first defeat since the opening day of the season as Jamaal Lascelles scored the winner for the second match running to help the Magpies to a third straight victory.
Hughes was not too harsh on his side after the result, but acknowledged that their level of performance dropped from last weekend's 2-2 draw against the previously perfect Manchester United.
"We didn't play particularly well today - I didn't think we were poor, we just weren't particularly as good as we have been in recent weeks, so that's the disappointment," he told reporters.
"We are going to face teams like Newcastle, who show us respect in terms of our ability and what we can do to teams and will sit back and invite us on, so we have got to be a little bit better and a little bit more accurate in our work and we'll be fine.
"The lad (Lascelles) scored against Swansea the other week as well, so we'd talked about his threat. But obviously the right ball right on to his head, it's difficult to defend under those circumstances.
"That was the disappointment because at that point, we had got back into the game and I thought we were growing into our performance and we may well have got something out of the game. But in the end, it wasn't to be."
The result leaves Stoke 13th in the Premier League table with five points from as many games this season.