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Simple: the Doctor essentially becomes a brand new person every time he regenerates, both physically and mentally. In the same way that Regeneration changes/rearranges/morphs his outer appearance, his insides and his brain are affected as well. He keeps the same memories but is a different man. The Tenth Doctor himself says that regeneration is really like a death and rebirth: "... Some new man goes sauntering off... And I'm dead." MrCatharsis 07:19, April 22, 2010 (UTC)

That and the Tenth Doctor was attacked by the Sister Cats in "New Earth". He had the same reaction to cats after that.So it was more of a distrust rather than a dislike.

I should also note that he didn't seem too unhappy at the sight of the half-human kittens in the car on "New Earth" in "Gridlock" so he doesn't necessarily dislike all cats.