1. Level3 started offering CDN services. By leveraging their existing peering relationships (as a tier 1 ISP) they could essentially subsidize the transit costs of the CDN business, compared to e.g. Akamai which had been paying Comcast for peering to reach Comcast customers.
2. Netflix got a good offer for CDN services from Level3, and switched a bunch of their content from Akamai to Level3's CDN.
3. Comcast therefore saw a bunch of paid traffic turn into unpaid traffic overnight, and complained.
This is a business dispute between two self-interested parties. Is it really fair for Level3 to use their position in the ISP business to undercut competitors in a new CDN business? Was it fair a few years ago when Akamai caved and agreed to pay Comcast for peering? Will it be fair for Comcast to use a newly acquired media property to exact revenge on Netflix/Level3?
The problem with Network Neutrality is that it takes a complex issue, the product of many complex business relationships, and frames it in a black-or-white context. The history here is complicated, and the only thing I'm sure of is that everyone's a bad guy sometimes.