AkrutoSync cannot sync over USB.
The two options available are syncing over the local area network (LAN) or via the Internet. If you are concerned with security, please note that all network communication is done over an SSL encrypted link. Also note that if you choose the option to sync over LAN, your data does not even pass through the Internet. You can connect your phone to your LAN by whatever means your phone allows, Wi-Fi being the most common one.