Well, the facts that he's made a habit of making himself unlikable and arrogant in public doesn't help his case. His remarks discrediting Gus' performance and generally insulting the likes of Hendo and Machida in the past didn't help, not to mention his dirty/classless tactics inside the cage (eyepokes, knee kicks, dumping Machida's unconcsious body, etc.) Also, getting UFC 151 cancelled and coming off as a complete hypocrite (rightfully) for his DUI and bogus faux christianity.
He's basically done far more to be a villain than a hero for MMA fans, even though the UFC has done everything it could to paint him in a positive light as a future face of the company.
There's also the fact his resume, while extremely strong on name value, is a lot less strong on context.
Let's take a look at his "legendary, dominant" run:
1) took the title from Rua, an undersized LHW with no TDD who was coming off a 10 month layoff and recovering from another knee surgery.
2) defended against Rampage, who he again held significant physical advantages over. This in addition to the fact Rampage hadn't had a KO win in almost 3 years, and in his last 4 fights had uninspiring wins over Hamill and Jardine sandwiching a loss to Rashad and an uninspiring win over Machida even Rampage felt he lost. In short: Rampage was well out of his prime long before the Jones fight.
3) defended against Machida, who stepped in on short notice to fill in for Rashad Evans. Lyoto's most recent win was against Couture, with his other fights before that being a controversial loss to Rampage, a KO loss to Shogun, and a controversial win over Shogun. Good win for Jones, even if Machida is a natural middleweight and was a late-notice substitute opponent whereas Jones had a full camp behind him. Machida was still relatively close to his prime, even if undersized and short notice. Probably the second best win on Jones' run as a result.
4) defended against Rashad, who Jones had huge physical advantages over again. There has been lots of talk regarding a possible move to middleweight for Rashad. Rashad also essentially gave up and went into survival mode after round 2, enabling Jones to coast to an easy win.
5) after the UFC 151 debacle, Jones rejects Chael as a late-notice substitute, despite Chael being a middleweight, an easy style matchup, and the fact that Jones had just completed a full training camp. Instead, he gets Vitor, another short-notice middleweight opponent with injuries going into the fight. Jones still almost gets his arm snapped off before finishing Vitor in the 4th.
6) despite the UFC's initial effort to reschedule the Hendo fight for the super bowl weekend card, Team Jones claims he won't be good to go by then due to his "arm injury." Instead, he gets middleweight/easy style matchup Chael, instead of Hendo, who also would have been good to compete in April and would have posed more of a problem than Chael. Jones then proceeds to smash Chael, but not before evading a possible doctor stoppage loss.
7) instead of a Machida rematch (which Lyoto had won two title eliminators to get), Jones picks Gustafsson, feeling that the less-proven Gus would be easily dispatched, and prove to be a showcase for Jones, proving that his dominance was built on allegedly amazing skills, not on simply being bigger than his opponents. Jones is a huge favorite going into the fight; most people accept it as a showcase for Jones. Instead, Alex destroys the script, soundly outboxing and mutilating Jones for 3 full rounds and 4:30 of round 4, all while Jones' supposedly godlike wrestling and ground game prove completely useless against the first opponent his size. Gus even shows himself physically stronger than Jones a couple of times. Based on being the champion and edging the last 5:30 minutes of a 25 minute fight, Jones gets a dubious decision most MMA fans disagree with, while being taken out of the arena on a stretcher.
8) rather than give Gus a rematch (which he deserves, considering, you know, most people with a functioning brain without an obvious dog in the situation feel that Gus won the fight), Jones asks for Teixeira, a much slower, shorter, less rangy opponent; in other words, a much easier style matchup then the disastrous blown cherrypick that was Gus. Despite giving immediate rematches in other controversial decisions (Shogun/Machida and Penn/Edgar I come to mind, with neither Edgar nor Machida looking like they'd been run over by a steamroller after the fight as Jones did.) The UFC gives Jones the Golden Boy his wish, despite Jones himself earlier taking a dump on Teixeira's credibility as a challenger and degrading Gus's performance in their fight.
So here's a good question: given all of the above, should MMA fans regard a man where all but one of his title fights were size mismatches (and three of them against middleweights in Lyoto, Vitor, and Chael, with Rashad being an additional future middleweight) in high esteem?
Bottom line, Jones got a lucky break and narrowly escaped with the belt against the only opponent he's fought he didn't hold every physical advantage over, and has also received extremely favorable matchmaking from the UFC brass based on the context.
Based on name value, Jones is the LHW GOAT. But he's nowhere close to being a P4P talent or an MMA GOAT in the making though, especially when its been vividly demonstrated how heavily he depends on physical advantages for his success, rather than, you know, actual skills. Unlikability has nothing to do with his not being regarded in the way his fans and the UFC would like you to view him (as an MMA GOAT in the making.) He isn't held in that esteem because his dominance is manufactured rather than natural, as Gus emphatically proved last week.