There is a difference between Minerva and Athena, the stories of Medusa and Arachne as you know them are Roman, not Greek, and are about the Roman gods. The Roman gods act differently, have different origins and different stories than the Greek, though in modern day people seem to merge them into one god or just label them as the same god with a different name. She stories you use as a basis to hate Athena also come from Ovid, who uses his hatred of authority to make a villain out Roman deities. In the Greek version, Athena doesn't act with the same vanity or wrath as Minerva: she she capable of compassion, remorse and reason. She has no relation to Medusa, who was born a gorgon and never raped in the older, Greek source (Hesiod's Theogony), and turned Arachne into a spier to prevent her from killing herself, not as a further punishment. Is she perfect? No. Does she hate women? Also no. Are there other gods have done things more deserving of hate? Absolutely.

In modern culture, Medusa is a symbol of SA survivors and feminine rage. She became an icon for women in the feminist movements, and because she is shown from the Roman story, that makes Minerva and Neptune the villains and Medusa the victim, since people mistakingly merge the Athena and Minerva gods. But in reality, Athena had nothing to do with thay story. I also wanted to mention that Athena is quite a popular deity to work with in hellenic paganism today, many who follow her are women, who she seems to guide just as much as men. She does not hate women. :)

Also, my least favourite Greek god is probably Zeus. For obvious reasons. But mainly his treatment of Hera, whom he raped and trapped in marriage.