Ummmm. You can be an good civ, but with massive amounts of ships. I don't see any restriction on that.
The reason that everyone attacks the evil is simple -- they're evil. Evil civs get bonuses, especially towards military power, so they need to be balanced out some way. And they're evil. The Ferengi aren't evil, they're neutral/greedy. They don't go tossing their citizens into death furnaces when fuel is low, but they don't stick their necks out for others either.
