The application or card issuer needs to be able to ensure that no one can tamper with the card. A perfect example is Mastercard. They want you to certify any applet that is loaded onto the same chip as their paypass applets. You also want to ensure that no one can delete the data on your the card. A smart card is considered a secure and trusted environment and part of what makes it so is the fact that once you deploy your application you can lock down the card to prevent modification.