No exchanges should be trusted with the amount you can't afford to loose. You must only store small amount for daily trading. If you want to trade big amount, deposit and exchange it ASAP.
To gain trust, you need to run as long as possible, no big and frequent disputes and it must be run by a trusted person. These don't prevent an exchange to run away, this will only help us to trade there.
People who ran those previous exchanges didn't have any such disputes I guess. Still they misused the trust as they failed to provide the level of security it needed to store those Bitcoins. The biggest example of which is MtGox.
Still don't get it how those coins were hacked without the interference of an insider?