In an age where printed periodicals were delivered by subscription, the subscriber information was available (and yes, often tracked by local and federal law enforcement), but not the specifics of what articles were read.
Today, with Web-based document delivery and Javascript instrumentation, the specifics of who reads what articles, time on page, sections read, interactions, shares, and more, are available not just to the publishere but advertisers, any entities hacking into or accessing their systems, app developers, and more.
And, yes, law enforcement, whether under warrant, subpoena, or ... other methods.
The subpoena, and USA Today's response [1] paints a picture of an incompetent and/or inexperienced FBI agent, who is unaware of existing Justice department guidelines specifically prohibiting her from serving such a subpoena.
Reading between the lines, citing "other methods" is the FBI's way of quietly withdrawing a subpoena that should never have been served.
[1] https://storage.courtlistener.com/recap/gov.uscourts.dcd.231...
> "The subpoena is being withdrawn because intervening investigative developments have rendered it unnecessary," an FBI spokesperson said.
I think this is nothing like a "mea culpa", but instead has absolutely everything to do with managing the establishment of precedents to work in the favor of the FBI whenever possible.