Antonio Rudiger, Danny Drinkwater, Pedro, Willian - from the spot - and Davide Zappacosta were all on target for Antonio Conte's side at Stamford Bridge in what proved to be a game to forget for the Potters.
After picking up four points from their two games either side of Christmas Day, Hughes's side end 2017 outside of the relegation zone but just two points above the drop following a disastrous run of six defeats in their last nine.
"It was a difficult day for us, clearly we were short of numbers in defensive areas, and we made a couple of mistakes too," Hughes told Match of the Day. "We need to get a few players back to give us that defensive solidity, we had two young lads in today, who tried their best in difficult circumstances.
"We had a few decent periods in the second half, when we managed to hold onto the ball, and I thought Saido Berahino looked sharp. We've got to go again on Monday - so that's why we had to rest a few players - so I take responsibility for that. If we win on Monday, it's a decent Christmas period for us. The schedule tests you and it will test us more than the bigger clubs, because they've got that squad depth.
"The reality was it was always going to be difficult to get a result here - even with a full strength squad - sometimes you have to be pragmatic."
Next up for Stoke is a home encounter with fellow strugglers Newcastle United on New Year's Day.