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The Doctor liked Jack Harkness well enough to let him travel in the TARDIS (end of "The Doctor Dances" to "Bad Wolf"). After Rose (as the Bad Wolf) unintentionally made him immortal when she resurrected him ("The Parting of the Ways"), Jack's presence made both the Doctor & the TARDIS very uncomfortable, as the Doctor explained to him in "Utopia":

JACK: ... I'm the man who can never die. And all that time you knew.
DOCTOR: That's why I left you behind. It's not easy even just looking at you, Jack, because you're wrong.
JACK: Thanks.
DOCTOR: You are. I can't help it. I'm a Time Lord. It's instinct. It's in my guts. You're a fixed point in time and space. You're a fact. That's never meant to happen. Even the TARDIS reacted against you, tried to shake you off. Flew all the way to the end of the universe just to get rid of you.

Their interactions thereafter indicate that the Doctor still likes Jack personally, though he doesn't fully trust him (shown when he disabled Jack's vortex manipulator again in "Journey's End"), but continues to have difficulty being near a person who's a fixed point.