I fail to see how CDNs and direct peering agreements between ISPs and content providers are particularly relevant to the debate over Net Neutrality. As an analogy:
Comcast owns all of the land and roads in a city (or region, or neighborhood). Google wants to deliver goods to customers in that city, but their warehouse is in another city. Google and Mom-n-Pop Content Provider, Inc. both use the same publicly funded highway to get their goods into the city, and the same Comcast-owned roads to deliver to customers throughout the city. Comcast can deliver goods faster because they have a warehouse in the city. So Google pays to build an air-delivery network (peering) and a warehouse in the city (CDN). I don't see the problem with any of this. The analog to net neutrality, then, becomes whether or not to allow Comcast to (abuse its monopoly ownership of the roads to) raise or lower the speed limit for individual delivery trucks, based upon whether or not they belong to Google, Comcast, or Mom-n-Pop.
As I've said, IANANE, so feel free to point out any relevant inconsistencies in this analogy. On an 'unrelated' note, Amazon...