It was because the Doctor left him for a reason but of course you'll know that by now, it was so funny though!
Yes, pure prejudice
But I suspect the Doctor really loves Jack, underneath it all. He switched remarkably quickly from faint disgust to relieved hugs, on telling Jack that Rose was still alive.
I'm hoping the Doctor's going to have a think about what Jack said to him about prejudice, and maybe examine himself a little. Particularly as Martha is now feeling a little bit jittery about the Doctor possibly abandoning her at some point (have a look at the official Martha Jones blog on Mypace).
I don't know where people get this idea about Jack being kind of evil. He's a hero! Yes, in Torchwood he has to make some pretty unpalateable decisions to save the world, but in the end, he is quite happy to give his life to save everyone. He loves a lot of people, but is intensely loyal in his own way.
I just think the character of Captain Jack Harness, whether he's being flirtatious and gung-ho, or moody and mysterious, is such a fantastic character and I can't wait until the next series of Torchwood. I think they've really got into their stride, and the last two episodes particularly, were absolutely brilliant. I particularly loved the episode
Captain Jack Harkness because it showed that our 'Jack' (or whatever his real name is) has a tender side to him. He actually cried at the end, did you see?
Personally, anyone who doesn't like Captain Jack is... What would you like? The moon on a stick?