I guess we will never know for sure what Bailey's intentions were but here's the controversy:
"The controversy centers on the early challenges to Smarty Jones in the 1 1/2-mile Belmont. With more than a mile to go in the marathon race, Bailey, aboard Eddington, and jockey Alex Solis, atop Rock Hard Ten, appeared to have prematurely moved their horses in an attempt to double up on Smarty Jones.
As soon as Purge started to fade, Rock Hard Ten and Eddington pushed to engage Smarty Jones rather than stalk him until the stretch run, putting pressure on Smarty and compromising their mounts in that pursuit.
Steve Waxman of Versailles, Ky., has been a racing fan for 45 years. The thoroughbred owner and breeder wrote that Bailey's ride was one of "not trying to win." He wrote that Elliott and Edgar Prado, who rode winner Birdstone, were probably the only two riders in the race riding to win. He concluded his letter by suggesting Bailey apologize to the Smarty Jones team.
Bill Brown of Philadelphia wrote that he watched the video replay of the Belmont Stakes five times, and is firmly convinced that Bailey and Solis had extremely "questionable rides."
Watching Bailey attempt to move five-wide aboard Eddington with a mile to go, he wrote, "left me incredulous ... indicating to me that (Bailey) was more interested in trying to get Smarty Jones beaten than to win the race himself."
Peter Thompson of Wellington, Fla., asked why Bailey would not sit behind the contested pace, but instead eliminated any chance his horse had of winning by pressing early.
And Mike Iammarino of Surprise, Ariz., wrote, "I have been a jockey for 17 years and have always had a lot of respect for Jerry Bailey. His ride in the Belmont Stakes, however, on a live contender, was a disgrace to horse racing. Bailey sacrificed himself only to beat Smarty Jones and jockey Stewart Elliott."
http://www.lasvegassun.com/news/2004/jun/14/columnist-ralph-siraco-smarty-jones-fans-cry-foul-/