The No. 1 overall pick has already missed six games this season and had just one tackle in his return from a knee injury last week.
Rapoport said on NFL GameDay Morning on Sunday that the coaching staff is becoming "frustrated" with the rookie, who didn't return from injury as early as they thought.
"What they want is for him to start showing some maturity and learn to play through these some of these ailments," Rapoport said. "As a source just mentioned to me, this is really the first time Clowney has faced any sort of injury adversity -- didn't really happen in college -- and they want him to try to play through it in the NFL, but they're frustrated with their No. 1 overall pick."
It's worth noting that O'Brien said Friday he wasn't frustrated with Clowney missing games, saying that injuries happen in the NFL.
NFL Media's Stacey Dales reported that after the pass rusher started feeling ill on Thursday and Friday, he came into the team facility Saturday and was not contagious, which showed some promise for Clowney playing against the Eagles, but it was not to be.
Certain injuries and illnesses aren't able be played through, but clearly some of the coaches believe Clowney could play and practice more than he has recently. Whether he suits up Sunday remains to be seen, but a message has been sent to the rookie.