The Potters went down to Oscar's goal in the first half and were unable to find a way past the Chelsea defence.
"Obviously it was a fantastic strike, but I didn't feel it was a free kick," Hughes told BBC Sport.
"We couldn't quite create enough clear openings. It was difficult for us but I'm pleased with what we did. We stuck at it and didn't go under. I'd suggest there were more positives than negatives."
Stoke return to Premier League action against Sunderland on Wednesday.