There are some basic programs that come with the flash thumb drives that can encrypt files in any directory you choose. This will prompt you for a password. If authenticated correctly, it will give you full access to the file. You may already have this if you own a flash drive. If you dont, u can probably find one on the net or go buy a thumb drive and move the program to you pc.
I can not think of any other way to protect the execution of the bat file. You could possibly set the file to only be accessed by certain users such as an administrator. Im not sure of your application so i dont know if that would work for you or not. Will it be on a end users desktop logged in under that users name, but dont want them to be able to execute it? If that is the case, you might want to try my original idea!