decrypt data in column before load into destination
When calls to decrypt methods return NULL, either the column is NULL or the account that is using the methods doesn't have access to the key.

From BOL


  Permissions
  
  Requires VIEW DEFINITION permission on the symmetric key and CONTROL permission on the certificate.


Look at at the account that is executing the SSIS package and verify it has the required permissions.

You can also launch SSMS as the account that runs the SSIS packages and try stepping through the underlying code of DecryptByKeyAutoCert. Something approximately like 

OPEN SYMMETRIC KEY MyKeyNameHere
   DECRYPTION BY CERTIFICATE Usercert;

SELECT 
    city_id
,   CONVERT(nvarchar(50), DecryptByKey(city_name)) AS city_name
FROM city;

CLOSE SYMMETRIC KEY MyKeyNameHere;