It's a anti-theft feature, it can not be disabled. The PCM must communicate with the PATS module or it shuts down the engine. I would suggest taking to Ford dealer and having it repaired, you probably have a bad key or transceiver. Make sure you are using a ford approved key. Have your battery tested, low voltage will screw that system up.
NOTE: Large metallic objects, electronic devices on the key chain that can be used to purchase gasoline or similar items, or a second key on the same key ring as the PATS ignition key may cause vehicle starting concerns and record DTCs under certain conditions. If a fault cannot be identified, examine the customer's key ring for such objects or devices. If present, inform the customer that they need to keep these objects from touching the PATS ignition key while starting the engine. These objects and devices cannot damage the PATS ignition key, but can cause a momentary concern if they are too close to the key during engine start. If a concern occurs, turn ignition OFF and restart the engine with all other objects on the key ring held away from the ignition key. Check to make sure the encoded ignition key used by the customer is an approved Ford encoded ignition key (encoded ignition keys from Rotunda, or Strattec are approved Ford encoded ignition keys).