netmeg - 1:13 am on Nov 27, 2012 (gmt 0)
Because many affiliates who use AdWords are thin affiliates, which Google does not consider to be a quality site. By definition, almost every manufacturer or merchant site is going to be considered more authoritative than an affiliate site.
If you are running a quality site that has a few affiliate links, you shouldn't have a problem.
But all you can do is test it.