Why does Athena hate medusa?

Athena was the one who cursed Medusa by giving her ungliness (snakes as hair, turn-to-stone eyes, etc.), after being Poseidon's lover whom he brought into one of Athena's places of worship.

Truthfully, the worst thing you can do by mythology about Athena is claim directly or indirectly to be better than her. Medusa didn't exactly do that. She insulted Athena by, um, doing some stuff with Poseidon in Athena's temple. Since Athena pledged to basically be a virgin forever, this romance didn't particulairly go down well with her.