The Rs have sunk back to the bottom of the table following a contest in which they were the better side for long periods, only to be undone by Charlie Adam's 52nd-minute strike. Adel Taarabt wastefully chipped over for the visitors and was unable to convert further opportunities after Adam's goal, while Asmir Begovic did well to keep out an Esteban Granero effort.
"We've had this conversation too many times after games unfortunately," Hughes said. "We played well as the away side - I thought it was a decent away performance. We restricted Stoke to very few chances. In general play I thought we were the dominant team in terms of how we wanted to get the ball down and play."
He added: "But the key at the moment is that we have to take chances when they present themselves. We created good opportunities, but unfortunately didn't take them."
Hughes was keen to defend Taarabt, rating the midfielder's overall performance as "really effective".
But the manager admitted a lack of a clinical touch had cost QPR, as well as hesitant defending for Adam's goal, with the ball being allowed to bounce through to the Scot when Jon Walters nodded a free-kick his way in the box.
"In fairness to Adel, I played him through the middle and I thought he was really effective," Hughes said. "He understood what was required, got in between the lines and was causing Stoke a real problem, certainly in the first half.
"If we had got a goal, I think it would have capped an excellent first-half performance for us, but it wasn't to be and you know that at those points in games, if you don't take your chances then there is always the danger you will concede at the other end."
Stoke boss Tony Pulis expressed some measure of sympathy for his fellow Welshman Hughes, although he emphasised the importance of grinding out results.
"We have played games this year that we should never have lost," said Pulis, whose team registered what was only their second win of the campaign and are up to 12th. "He (Hughes) will be disappointed, with the chances they have created today, that they haven't scored some goals. But you need to eke out results."