The Doctor doesn't "hate" Captain Jack.
Initially he disapproved of Jack's con game in "The Empty Child"/"The Doctor Dances". Then, as he explained to Jack in "Utopia", when Rose/Bad Wolf brought Jack back to life (in "The Parting of the Ways"), she unintentionally did so "for all time", instead of just once, thus making Jack a "fixed point in time". A Time Lord perceives a fixed point differently from other things, with the result that, at least initially, the Doctor felt extremely uncomfortable around Jack. The TARDIS, which is even more sensitive to temporal oddities, was so uncomfortable in Jack's presence that she fled to the end of the universe to try to get away from him (also "Utopia"). Later, he was wary of Jack's association with Torchwood Three, because of what Torchwood One, the parent organisation, did during "Army of Ghosts"/"Doomsday" -- especially of how they treated him & Rose -- & because those events cost him Rose, for which he blamed Torchwood. (Torchwood had also been at least partly responsible for the events of "The Runaway Bride", as they were the ones who drilled down to the Racnoss.)
It should be noted that, later on, both the Doctor & the TARDIS seem to have become more used to Jack & no longer made so much effort to avoid him ("The Stolen Earth"/"Journey's End"). During the Tenth Doctor's "farewell tour" at the end of "The End of Time", he even sought Jack out & set him up with the opportunity of a date with Midshipman Frame.