The Cameroon international seemed to be the target of persistent boos by the Burnley faithful in the wake of his racism row with West Brom striker Jay Rodriguez, who started his career with the 'Clarets'.
After an investigation, the FA found 'no proof' to support Bong's complaint and subsequently dropped all proceedings. Although they did stress that the defender made the complaint in good faith and "there was no suggestion that it was malicious or fabricated".
It didn't stop the jeering from Burnley supporters though which Hughton hit out at during his post-match press conference.
He told reporters: "I thought the reaction of the Burnley supporters towards Gaeten every time he got the ball was shameful, I really do. I was incredibly surprised, I must admit. I certainly didn't expect it here.
"They should look at the two statements that came out afterwards - one from the independent committee and one from the FA.
"As regards his performance, it's nothing short of what I expect of Gaetan. He's an incredibly disciplined and straight individual - as honest a person as you will meet.
"It's something that happened, it's not nice at all. But, of course, he's big enough and strong enough to cope with it as showed by his performance," Hughton concluded.