Well, there's no gold standard for how any of the contracts are setup, but if I had to guess, it's because you're talking about Level 3 <-> Comcast. The profile of Netflix is far different from Level 3. Generally the fee is based on the net (as in net total, not net internet) traffic.

If Level 3 sends 100Mbps to Comcast, and Comcast sends 100Mbps back to Level 3, or at least approximately even most of the time, they very well may have a settlement free agreement. This is believable because Level 3 is a transit provider, as in if you send them traffic bound to anywhere on the internet, they'll get it there, so the amount of traffic that Level 3 receives from everybody to get to Comcast could be roughly equal to the amount of traffic Comcast wants/needs to route through Level 3 to the rest of the internet.

In the Netflix<->Comcast case, it's not a transit peering. Netflix can only send traffic over that link that is destined for Comcast customers. These peering arrangements are generally drastically cheaper per Mbps than the transit peering. The difference here though is that the only think Comcast sends to Netflix is HTTP request for the most part, and then Netflix sends a video stream back, so there's a HUGE imbalance in the traffic going each direction.

All that said, what Netflix pays to Comcast may scale with Comcast's costs, but there's no direct relationship. To simplify it a bit, Netflix is paying to get traffic to the Comcast central brain. Customers are paying Comcast to get a pipe laid connecting them to the central brain. The two costs are not very directly related.