Goals from John Terry and Cesc Fabregas secured all three points for Jose Mourinho's side at the Britannia Stadium, but Hughes was pleased with certain aspects of his side's display.
However, the Stoke boss admitted Terry's goal in the second minute was a bitter blow to their plans and as a result allowed Chelsea to dictate the tempo.
"That [Terry's goal] was the worst outcome of the opening period," he told Sky Sports. "It was the one thing we wanted to avoid because we know Chelsea can play counterattack, they are adept at it, they can kill the game.
"We gave it a real go in difficult circumstances, we got on the ball, asked questions, and gave good account of ourselves.
"I thought before their second we were putting them under pressure, but they are very good at killing the game, more often than not they took the sting out of the game, it is experienced play, they understand what is required.
"We had a go against a team that many feel will win the league.
"We tried to take the game to them, we kept them down to few opportunities, they took two and that's enough for them. But we have to take the positives out of it and move on."
The result leaves Stoke in the bottom half of the table ahead of their trip to Goodison Park to face Everton on Boxing Day.
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