I think “hate” is too strong a word, honestly. The TARDIS is wary of Clara because she recognizes her.
Spoilers from “Asylum of the Daleks”, “The Snowmen”, and “The Name of the Doctor”:
It’s established in “The Name of the Doctor” that a Gallifreyan splinter of Clara nudged the Doctor into choosing the TARDIS he did. It’s not clear how this meshes with the TARDIS’ own statement that she chose the Doctor, but leave that aside for the moment. Chances are also good, though not firmly established, that the TARDIS was at least somewhat aware of Clara’s “impossible” nature and constant recurrence throughout the Doctor’s life, even though the Doctor himself only became aware something was up beginning with “The Snowmen”, when he made the connection between Victorian Clara and Soufflé Girl.
The TARDIS would clearly recognize that only something fairly bizarre and catastrophic could cause Clara to keep recurring like that. Something wibbly-wobbly and timey-wimey. Thus, when Clara began to actually travel with the Doctor, the TARDIS would be understandably nervous that the catastrophe that led to all this was imminent, and thus be not entirely keen on having Clara around.