Oussama Assaidi put Stoke ahead four minutes into the second half at the Britannia Stadium, before Jermaine Pennant hacked down Leon Osman in the area to open the door for Leighton Baines to equalise from the spot.
But Hughes feels his side coped well with Everton for the most part, and conceded that the penalty was justified.
"We're disappointed," he is quoted as saying by BBC Sport. "We put a huge effort in. We were good value for a 1-0 lead.
"I felt we coped really well with Everton. Four or five weeks ago we were beaten 4-0 by them. Today we more than matched them.
"It's a clear penalty. We made a mistake and it allowed them a way back.
"I thought we deserved three points. We played really well."
The Welshman praised the contribution of Assaidi and refused to rule out any activity in the January transfer window.
"Oussama Assaidi has been a real asset into the last few weeks," he added. "Teams are looking to double up on him.
"(In January) we'll see what's available. It's not easy. Nothing is in the offing yet.
"Everyone is working hard, as are we to add to the squad to take us through to the end of the season."
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