When a brand decides it wants to properly attack its marketing, it seeks out experts to help them do so. Sure, they may have a marketing manager in-house to oversee the marketing process but when they need heavy lifting in the form of an integrated advertising strategy that plays out across multiple media in multiple markets, they turn to an advertising agency.
It's no different when a brand decides to enter the affiliate marketing channel.
Many merchants entering the affiliate channel believe a workable solution is to delegate all affiliate marketing responsibilities to an in-house affiliate manager and/or hook up with an affiliate network's managed services offering. But an affiliate manager is just one person and an affiliate network is just a platform, a technology provider and not a marketing expert. Much in the same way Google Search is a platform for search engine marketing and does not offer search marketing expertise.