If by "protect" you mean "how to hide affiliate url" then you can not do that. When you buy any product, if you scroll down on Clickbank checkout page, there will always be the name of the affiliate.
I use htaccess to hide affiliate links...but there's no foolproof method with clickbank. If someone is really determined they can figure it out and use their own aff link.
I literally just posted this in another thread... In your htaccess file, add a line like this: Redirect /merchant http://www.merchantsite.com/aff-link then whenever someone clicks on a link to yoursite.com/merchant they'll automatically be redirected to http://www.merchantsite.com/aff-link It'll be seemless from the visitors point of view and you'll be hiding your aff link from commission plunderers.
If you have Cpanel hosting, just made a redirect using Cpanel. It will add the line to the htaccess file itself