This is just a framing issue and I don't get the hate here. It would make sense that ISP's openly decide to charge flat rates to users while charging special fees to really large content providers. What's ridiculous is that this is being settled in courts of law, as if someone did something wrong, instead of being just business deals.
Internet infrastructure and usage is relatively recent and quickly shifting, so the social/political/economic aspects are always trying to fit into legacy arrangements. In this case it was easier to preserve the ISP-user agreement of how content is served and billed, while using pre-existing infrastructures (courts of law) to settle who actually pays the extra bills. It feels out of place, but if you strip the legal content out it's just business deals about services.