The immobilizer requires successful reading of the RFID chip inside the key. There is a pickup coil around or beside the ignition switch. If that pickup coil is damaged, or there is metal between it and the key, the immobilizer won't work.
This is the Passat B5 forum; your 2006 model is a B6, so I don't know exactly how the pickup coil is configured in your car. Someone else on the forum may know.
The other option is an immobilizer delete, where the immobilizer requirement is "coded out" of the ECM, if that's available in your country.