Persephone decided to destroy the tower that held up the world or something because she felt like she got really screwed over by the Olympians as well. Kratos ended up having to kill her to save the world (while abandoning his daughter forever) and putting Atlas in the position that he holds now: Holding the world up.
Hades being pissed at Kratos is addressed in the third game. Before his boss battle Hades talks about "Grievances" that Kratos has committed against him (killing his niece Athena, his brother Poseidon and his queen). Predictably the battle does not go well for the Lord of the Underworld.