More likely, they had taps but did not know what they were talking about. It was widely reported that, pre-9/11, Arabic translators were scarce in most Western intelligence services including the US, since their traditional focus were Russian, Eastern-European languages, and Chinese. You just need basic informal codes for most logistic purposes (which would be mostly "I've done this, I've done that" to confirm timings and prepare the next steps, rather than "I will hijack a plane and crash it into NYC" which would have been agreed beforehand) to make it very difficult for people who might not know all the intricacies and slang of regional Arabic varieties.
So the NSA might have known these people were learning to fly and maybe even preparing a hijack, but until 9/11 this was not dramatic -- if and when the hijack happened, they would have been expected to fly to Cuba or something and then dealt with. Pre-9/11, airplane hijacks had become rare since their '80s and '70s heydays, maybe there was some complacency (as in "yeah these guys will never manage it, and even if they do, we'll likely get most passengers back safely anyway, let them play"). Or at least that's what a sharp Occam's razor would suggest.
Old style hijack had become rare because police forces around the world made sure that you couldn't come out a winner, you typically get killed. Hijacker are at a disadvantage: limited resources, stuck in a small space easy to surround.
The fact that the 9/11 highjackers had planned to die as part of the hijack was a game changer.
Exactly. A 9/11 style attack is also a single time event. Now that passengers know the outcome, they simply will not let it happen again. The only possible method would be to turn an existing pilot into a suicide killer.
The reinforced doors they introduced after 9/11 make this strategy particularly good. The passengers can't do anything if the pilot decides that he has a death wish.
An example of such would be the Germanwings Flight 9525 crash from May 2015, where the copilot locked the cockpit door after the pilot left for a bathroom break and then flew into a mountain.
Crashing highjacked planes was a known scenario. In fact, FOX broadcast a fictionalized scenario where a commercial airliner was highjacked and set on a crash course with the WTC about six months before 9/11/01.
Tom Clancy's wrote a fictional book about lone mentally disturbed Japanese pilot flying a plane into the pentagon. I read it that book maybe a few weeks before 9/11. Was shocked that the US intelligence didnt see something like this happening when a fiction author did.
Edit: the author of your link addresses the episode in the comments section, "The Lone Gunmen Pilot Episode", and says that the article you linked was only focused on things "in production" when the attack occurred.
Wow, I had forgotten that series (X-Files spinoff).
Vince Gilligan was an Executive Producer.
The actor playing the father, George Coe, was one of the original Not Ready for Prime Time Players on SNL, then later played Ben Cheviot on "Max Headroom".
So the NSA might have known these people were learning to fly and maybe even preparing a hijack, but until 9/11 this was not dramatic -- if and when the hijack happened, they would have been expected to fly to Cuba or something and then dealt with. Pre-9/11, airplane hijacks had become rare since their '80s and '70s heydays, maybe there was some complacency (as in "yeah these guys will never manage it, and even if they do, we'll likely get most passengers back safely anyway, let them play"). Or at least that's what a sharp Occam's razor would suggest.