You can protect your cryptocoins by not keeping them on the exchange. There are now excellent hardware wallets available for bitcoins and many altcoins.

Trust in a third party is a security risk. If you leave the coins on an exchange you are trusting them. Just as you do if you leave your money in a bank. It can be even more risky because many exchanges do not have the same experience with security and the insurances against theft that banks may have.

Even if today the security and protection of the principal bitcoin exchanges is considerably better than MtGox.