Fulham could have recorded a sixth straight home win, but Chelsea keeper Petr Cech saved a stoppage-time penalty by Fulham’s Clint Dempsey.
Hughes said: “Given the circumstances at the end, it’s disappointment.
“We came up against a strong Chelsea side who posed questions of us in the second half, and we had to be strong and resilient.
“But it was a real opportunity to beat a very good side at the end.
“We’ve been playing well of late and showed real character to dig in and create chances at the other end.”
Hughes claimed Dempsey’s penalty should have been retaken.
“Drogba was encroaching in the box,” he said.
“Mike Dean saw it: he was alongside Clint as he kicked it. Mike Dean saw that, so it should have been retaken.”