you are charged extra, still, if you tether using the USB connection.
the wired-tethering option is available on the phone for devices that don't have a receiver in them to accept wireless signal for internet (ie a computer that does not have a wifi receiver built into it. you could run your usb cable from your phone to this computer & give it internet access). this is why the option is still charged as a feature if it is used.
you are only charged when using the Verizon method of wired tethering.
however, using an app like pda.net will not automatically add that charge to your account. IF verizon notices large amount of data suddenly being used on your account vs your usual consumption, then they may investigate. unlikely, but still a possibility.