Saturday's 3-1 defeat to United was the Cottagers' third loss in the space of a week and the poor run has seen a number of fans turn on manager Jol, as well as some of the Fulham players.
Ruiz, signed to much fanfare from FC Twente in 2011, has struggled this term and his 74th-minute substitution was met by loud cheers followed by boos.
The Costa Rica international tweeted later that night: "I want to thank those who are supporting in this difficult time."
But Jol was angered by his treatment, and he 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."
Ruiz's lack of consistency and knack of losing possession has frustrated many, but Jol warned Fulham would miss him if he left.
"Sometimes he is a my best player and sometimes gets caught on the ball," he said. "There are a few other players in the past like him and I think one of my heroes is Glenn Hoddle.
"People never gave him credit because sometimes he was a bit like Bryan.
"They have to get used to him and if they don't get used to him, we've got a problem because I need Bryan Ruiz.
"Maybe they don't need me. They need Bryan Ruiz, believe me."