I’ve worked with netflow data before. All it says is time, source IP, destination IP, protocol, source and destination ports, amount of data transferred, and a guess at what type of traffic it is (http, torrent, video stream, etc). cisco.com/…/technologies_white_paper09186a00800a3… (table 6, though most of the fields in that table aren’t actually used). It doesn’t include any of the data within the connection.
It wasn’t previously just your ISP, it was every provider between you and the endpoint. That is, your ISP, their ISP, and the multiple backbone providers with the big pipes between ISPs (these are the ones selling the data in the article). And of course the NSA because they have a direct tap on the backbones, but they don’t share that access or data with anyone.