The former Manchester City manager, speaking to reporters after the game, also believes that the referee made a "poor decision" in sending Steven N'Zonzi off.
"Unfortunately the best team didn't win," Hughes said after Stoke's third consecutive 1-0 away defeat. "We are disappointed that a performance of character, desire, determination and no little skill got no reward.
"On too many occasions this season we have been hurt by refereeing decisions and been left with a mountain to climb. All you ask is for a level playing field.
"I feel it was a poor decision by the referee [to dismiss Nzonzi]. It's difficult for him because [Jozy] Altidore went down very easily and on the night too much of that was going on."
Stoke currently occupy 16th place in the Premier League table, three points above the relegation zone.