Apple MFI: Is there any fee for entering the program?
You have to purchase a credit review and have your credit approved in order to enroll in the program.  That is the only cost to enroll.  

Be aware that this is for large companies that intend to sign an NDA, receive Apple confidential information and pay royalties for access to and/or participation in the program.

The credit check is required so that Apple can ensure your company has the financial resources to bear the costs of participating in the program:

From http://mfi.apple.com/faqs :


  Why do I need to complete a credit review?
  
  A credit review must be completed in order to determine your company's
  ability to meet the financial obligations associated with the MFi
  Program.