Yeah, Jon knows his limitations better than his fans. Jones fans are 100% sure he can beat anyone, but Jones himself is not so irrational. He does not fear Tom in the sense of getting hurt by him, but he fears the loss, and how that will reflect on his career. Jon knows being a guy that barely got by mediocre LHWs, he's not going to do well with serious challenges at HW. It isn't complicated.
Jones knows it is a different ballgame fighting bigger fighters with similar skill levels, and that is a losing proposition even if his fans can't see it; these are challenges he has never faced. A straight comparison of quality of opponents is goofy when one of them was fighting a weight class up, especially HW which has less of a ceiling.