Some have weak encryption, aren't up to date with all the patches, don't use 2FA, are vulnerable to DDOS attacks, are vulnerable to SSL CRIME attack, ect....
The bigger threat is still the owners running off with the money though. I would only trust either a well regulated exchange in a country that prosecutes thieves like the US or an exchange that is insured or are using other means of protecting their clients like muti-sig authentications. Even than so I would still suggest securing your assets yourself and only using exchanges as a place to perform the trade.
well said