The Potters were cruelly denied a much-needed victory as Leighton Baines converted an injury-time penalty to cancel out Liverpool loanee Oussama Assaidi's 49th-minute opener which left Hughes to ponder what might have been.
"Well, you get to that stage of the game when you think you've seen the game out," he told Sky Sports.
"I thought we'd played really well today, great in every aspect really - (we were) on the front foot and bounced back certainly from a poor performance against Spurs (3-0 loss on the weekend).
"But today we were right on the money I felt and really restricted Everton to very few real clear-cut chances.
"I felt we were always in the game in terms of possession and chances created, certainly in the first half, I thought we were excellent.
"Towards the end of the second half, obviously we were 1-0 to the good and they started throwing people forward so we had to just dig in and try and protect what we had.
"Unfortunately we made a mistake and conceded a penalty and they were able to take something out of the game.
"But in terms of the game as a whole, I felt we deserved three points today."
For breaking stories and all the great banter like us on Facebook: facebook.com/tribalfootball