Even exchanges with a good reputation have been "hacked: and stolen money from their customers. No matter how reputable an exchange is the coins aren't truly yours unless you hold the private keys yourself.
One might even almost say that even an exchange with a shitty reputation, yet somehow finds a way to let people keep custody of their own private keys (without ever needing to share ownership with anyone else), should get first pick over a reputable exchange.
Besides, reputations are only as good as their last good/bad action.
Although, cryptopia really seems to have survived more than its fair share of bad reputation events cause people keep coming back to every new version born from the ashes of the last.