They obviously resigned because George W. Bush is an anti-semitic environment-destroying SUV-driving children's-lunch-stealing slave-owning gay-bashing senior-citizen-beating reincarnation of Adolf Hitler. If you think otherwise, you're a part of the vast right-wing conspiracy.
In all seriousness, there's really no reason to look closely at their resignations. Fleischer's deputy is taking his place, which doesn't really seem like something that would happen if he was fired. Generally if you fire someone, you get rid of their co-horts as well.