I guess it would have been a less compelling story if it didn't have the anti-advertising bent, and was more along the lines of "NSA uses web analytics cookies to pinpoint users."
Uniquely identifying web browsers by assigning a unique ID into a cookie has been a core behavior of the web analytics industry for over 15 years. You want to know how many unique visitors are coming to your web site? Assign an ID!
If advertising didn't exist, and Google remained the most popular website, the NSA would still have a unique client identifier. They'd also probably have more details, since the main alternative to advertising is subscription, which would require (with current technology) disclosure of actual personal information.