The main plugin uses the Block.io API & wallet service. Communication between the plugin and the API is secured via 4,072 bit SSL keys. All data stored at their service is encrypted. Multi-signature wallets make it impossible to move the coins without your signature. Read more about security at Block.io.
If you want to reduce the influence of third parties even further you can use our HD wallet add-on. It enables you to accept payments directly to your own HD wallet without any middlemen between you and your customers.