I used to work at VigLink and previously worked at Rakuten, the parent company of LinkShare. Excepting a few instances (see bottom of this post), you should use VigLink (or similar) for a few reasons:
1. if affiliate is not your sole and primary business, you should use one of these solutions so you can become great at your core business while picking up this revenue
2. it's a pain to manage affiliate relationships especially at the outset -- fast-track that process by using an aggregator.
3. starting out, you will get vanilla rate-card affiliate rates if you go direct. Aggregators will often have premium rates so that you net out better than you would have going direct.
4. By working with an aggregator, you will be approved for a lot of affiliate marketers who would otherwise ignore you as low-traffic startup.
5. Once you are up and running, you can start cherry-picking the best performing marketing relationships and take them direct on preferential terms and cutting out the middle-men (i.e. focus on the important relationships when they are at scale - let the aggregator monetize the rest for you automatically)
6. there's a technical and operational debt you incur by integrating with all the networks directly - you have to be operating at significant scale (in affiliate terms) before you can really justify going direct to any one network.
Unless you are focused on just a very small number of marketers in a specific non-retail category (e.g. you have some insight into how to market more effectively to credit card or insurance shoppers) then you should really think about the aggregator route. If I were to go into the publisher business again promoting merchandise, an aggregator would definitely be part of my initial plans.
