Jol, who has come under fire himself this season, was dismayed to hear cheers followed by boos when Ruiz was substituted in the 74th minute.
The Dutchman has urged the club's supporters to get behind his playing squad as Fulham seek to bounce back from three defeats in a week.
Addressing the crowd's criticism of Ruiz, Jol said: "It was very disappointing. 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."
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