Affiliates practice link cloaking for a number of reasons:
It’s a consumer-friendly practice. A URL that contains the merchant’s name makes it more comfortable for consumers to click on the link.
To hide the affiliate’s identity. Cloaked links can hide unsavoury search marketing tactics and keywords from you, the merchant.
To protect against commission hijacking. Some affiliates worry that spyware running on a consumer’s machine will replace their affiliate ID with the ID of another affiliate, thus hijacking their commissions.
To boost quality score. Google doesn’t seem to like affiliates very much which is very apparent in the low quality scores of many affiliate ads. Think about a landing page with nothing but ads and affiliate links that take the consumer from an Ad Words listing to a landing page and then immediately through an affiliate link. Cloaking the affiliate link is a method used to beef up the quality score in this scenario.
Tracking: It is easier for the affiliate to track clicks and visitors when using its own URL.