It's not that hard to understand why. Having a computer connected to the net to run bitcoind means that if you get it rooted by any chance, you just lost the entirety of your hot wallet.
Please, please stop doing that.
And if you send the balance to an off-site wallet every hour, or less, then you aren't exposing much of your balance anyway. If you're an exchange, it gets a lot harder since you have to figure out how much to keep on a hot wallet. But if you're just accepting Bitcoins, there's little to no risk, as long as you regularly send your balance off-site to a cold wallet.
And if your web server is rooted, then they've got any balance you've exposed to your web app, regardless of whether you are running it on bitcoind or some third-party web service.
I recommend cold wallets instead. You can have your server rooted and not lose a satoshi.
At the time, Roman Shtylman, the founder of Bitfloor, described it: “last night, a few of our servers were compromised. As a result, the attacker gained accesses to an unencrypted backup of the wallet keys (the actual keys live in an encrypted area). Using these keys they were able to transfer the coins. This attack took the vast majority of the coins BitFloor was holding on hand.”
So it was a storage issue and had nothing to do with what we're discussing, which is how to process Bitcoin transactions. Which brings me to the question: how would you process transactions on this cold wallet you speak of? Somewhere, you have to have either bitcoind or libbitcoin running (and most business will avoid the latter because it's AGPL, unlike bitcoind which is under MIT license).
To be clear, I strongly agree with the suggestion to keep as much money as possible on cold wallets. If you are just accepting Bitcoins for payment, this can be virtually 100% of your coins. As long as you are regularly moving your coins off of the bitcoind daemon connected to your web app, you are risking very little. Hell, you can transfer the balance off-server every minute if it makes you sleep better.
How do you accept bitcoin? Please enlighten us.
I didn't say you shouldn't use wallets, just don't use the naive approach of having a plain wallet in a computer that's exposed via bitcoind. That's asking for it.
Cryptography is hard, but you can use this for instance:
http://bitcoinarmory.com/using-offline-wallets-in-armory/
It's already prepackaged for you. Give it a good read if you don't know it. Free, Open Source, etc. And the author is a nice chap.
It's not the only way. But whatever you do, just don't keep a massive hot wallet in a server that's online. They will find it and if you move enough money they will put massive amounts of effort into hacking it.
EDIT: BTW, you do realize that Armory is a front-end to bitcoind, right? You still have to run bitcoind for Armory to work.
From their Github page:
"Armory has no independent networking components built in. Instead, it relies on on the Satoshi client to securely connect * to peers, validate blockchain data, and broadcast transactions * for us. Although it was initially planned to cut the umbilical * cord to the Satoshi client and implement independent networking, * it has turned out to be an inconvenience worth having. * Reimplementing all the networking code would be fraught with bugs, * security holes, and possible blockchain forking. The reliance * on Bitcoin-Qt right now is actually making Armory more secure!"