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Disclaimer: I don't own the awesomeness that is Doctor Who. That belongs to the BBC.
What is That Feeling?
Captain Jack Harkness knew he could be a bit of a flirt at times, but it took him a bit for him to figure out why the Doctor always got so mad at him for it. At first he thought the Time Lord was just being a prude, but after a short time on the TARDIS, Jack knew that thought was wrong.
He noticed the way the Doctor and Rose interacted, the way they would flirt with each other.
Jack was by no means dumb, and so he deduced that the reason the Doctor got mad at him for flirting with Rose was simple: he was jealous.