If you run a bitcoind property it can be incredibly difficult to hack and empty all your coins. A web wallet all you need is a username and password. If you get into the web site it can be extremely easy to find those things. With a bitcoind you can set a lot of parameters both in the bitcoind and OS itself to protect it. I am not going to go into detail because I don't have time to write it all out. If you want to pay me I can it setup and make it very difficult to be hacked.
Cause you would have an IDS and you have bitcoind set to the server ip which gives you more time, to pull it offline, where a web wallet, they can steal the coins quicker. Hence why I said more difficult to steal coins and not impossible to steal coins. Which you are confused with if you read your question.