An anti-Wenger banner that read 'Arsene - thanks for the memories but it's time to say goodbye' was unfurled during Arsenal's 1-0 win over West Brom at The Hawthorns last Saturday.
That victory was followed up by another 1-0 success at home to Southampton on Wednesday, leaving Arsenal in sixth place.
And with Stoke and Arsenal set to meet at the Britannia Stadium at the weekend, Hughes has come out in support of Wenger.
"I'm a little bit wary of things like banners," he said in a press conference on Thursday.
"It's two or three guys holding up a comment. No one knows the percentage of fans who think in the same manner.
"It's quite possible it's not representative. He won a trophy last year.
"In football sometimes familiarity brings contempt. Maybe some people want a change for change's sake. Sometimes you have to be careful what you wish for."
Hughes revealed that midfielder Glenn Whelan was unlikely to feature on Saturday as he continues his recovery from a calf injury, and there are doubts about Jonathan Walters and Stephen Ireland.
"Glenn Whelan is progressing," the Welshman added. "The calf muscle is inflamed and we hope, if he has to miss one more game, he should be all right for the rest of the season.
"It is undoubtedly the worse run of injuries that I have had during my time at the club, and when you consider the fact that we have had a bout of illness going around the place too, we have been unfortunate.
"Stephen Ireland has picked a bit of illness up today disappointingly, because we thought we had seen the last of that.
"Jon Walters didn't train today, so we will have to see how he is a bit closer to kick-off. Hopefully he will be back available to us."
