Goals from Roberto Soldado, Aaron Lennon and Mousa Dembele secured a comfortable win for Tim Sherwood's side and saw Stoke, who were beaten 5-1 at Newcastle on Thursday, slip to a second heavy defeat in succession.
The visitors struggled to retain possession at White Hart Lane and only managed to muster one effort on target, through Peter Crouch in the closing minutes.
Stoke did see a penalty claim turned down following a Michael Dawson challenge on Oussama Assaidi, but Hughes acknowledged his side's performance was not good enough.
"I felt a little bit aggrieved at the start of the game. I felt we had a good claim for a penalty before Tottenham's penalty," the Welshman told Sky Sports.
"In terms of having an impact on the game, we found it difficult.
"They are a good side and move the ball around quickly. They have got a lot of power and pace and at times we struggled to cope with that.
"There are reasons for that as we are missing key players but we need to do better. On the day we were not good enough and they were significantly better than us.
"At times we need to get behind teams and at the moment we haven't got that option. That makes it difficult for us."
Stoke sit 12th in the Premier League and will begin 2014 by welcoming Everton to the Britannia Stadium.
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