It would protect against what happened with MtGox -- if, after losing some but not all customer funds, they tried to keep running the site to make back the money. It would protect you from putting money into a site that is already bankrupt.
There are more sophisticated schemes that allow you to check the amount in your account, and verify that your account was included in the total, without seeing the size of other accounts: https://iwilcox.me.uk/2014/proving-bitcoin-reserves .