David Murphy gave Blues a 20th minute lead at Stamford Bridge but Chelsea saved their blushes with a second half Daniel Sturridge equaliser to earn a replay at St Andrews.
"We had players out and then we lost Stephen Carr so early in the game, that was a big blow, but we have had to cope with a lot of things today," the Blues boss said after the game.
"We also had to cope with a very, very good Chelsea team that caused us problems, but I thought that for large parts of the game we were able to cope with those problems and pose an attacking threat ourselves.
"I'm more delighted not so much with the result as the performance," Hughton added.
"A Premier League team playing against a Championship team at home are always going to be favourites.
"Any unrest, it's normal, but I'm quite sure that they'll go on to have success because of the quality of player that they've got."