A section of the Potters' following at Craven Cottage jeered Richard Cresswell from the field as he was replaced during the second half of the 1-0 defeat.
Pulis feels the treatment handed out to the striker was uncalled for, insisting the experienced frontman should be given more respect for the part he has played in the club's recent successes.
"It is disappointing. You do not want to hear that - certainly not at the moment when our supporters are getting so many plaudits," said the Stoke boss.
"I thought Richard did well, he worked hard. He puts in a shift all the time and is an honest kid.
"He came on a free transfer and has been a great signing.
"He helped us get promoted and fingers crossed he will help get us established in the Premier League.
"For that people should respect him and get behind him."