Hughton took the decision to remove the striker in the 70th minute and replace him with Swedish international Johan Elmander, which was met by jeers from certain sections of the home faithful.
"It was about fresh legs. That was Gary's second game after being out for a chunk of the season. I never have any problems with the reactions of the supporters because this is their football club and they care deeply," the Eastern Daily Press quotes Hughton as saying.
"What they are is fanatical and passionate and any frustrations they express is to see us win and I share the exact same frustrations. They are the decisions I have to make. I know the team, I know the balances and the players we have on the bench and I felt we would still create enough chances and have good possession of the ball.
"Gary did well. He is up against two big, mobile centre-halves and you want a contribution but he looked sharp, his link up play was good and he got himself in behind. He started later than anybody else because of the injury in pre-season but we hope to see more from him."
Hooper joined the Canaries in the summer from Scottish champions Celtic.