Ruiz has struggled to impress for the Cottagers this season, and the stadium announcement of his 74th-minute substitution at the weekend was met with cheers by the home fans before they turned to boos.
"It was very disappointing," Jol said of his treatment. "That [kind of abuse] is something I can cope with because I know football. I have been involved in 1,300 games and I know if people are not happy, they will give you stick.
"Bryan is a player that came back from Costa Rica's game against Mexico; he scored, they won 2-1 and he goes to the World Cup. Then to come here and get that sort of contradiction [in reception]: over there he is a hero and here they boo him off the park.
"That is very, very frustrating for him and very disappointing for me. I wanted my supporters to stay behind my players. He is an unbelievably nice person so I had to whisper a few words in his ear. I said he is arguably my best player and that he should know that. It doesn't mean anything but at least a couple here, and I am one of them, trust him."
Ruiz joined Fulham from FC Twente in 2011.