Hughton's men fell 2-0 behind after less than an hour as Morgan Schneiderlin and Rickie Lambert put Southampton in command.
The 55-year-old responded by bringing on Ricky van Wolfswinkel, Nathan Redmond and Johan Elmander in a triple substitution that attracted the ire of the travelling supporters at St Mary's Stadium.
"It's never nice (being criticised), but I understand," Hughton said.
"We had more than 2,000 supporters travel down and it's their club and their team and they want to see a Norwich team which is really competing and allowing themselves to be really competitive in the game.
"What they saw for longer periods was a Southampton team that is better than us.
"It's not nice, but as manager you have to take all criticism on the chin and look for a response in the next game."
