Because Foreign Affairs ran an article headlined "Afghanistan, Graveyard of Empires" in November 2001, after 9/11 and the beginning of Operation Enduring Freedom. Later writers (who are within the 20 year rule and typically talking about things within the 20 year rule; i.e., Operation Enduring Freedom's later phases and subsequent operations) kept using the phrase, and now it is used as a kind of shrug. "I mean, everybody's known for millennia that Afghanistan is the graveyard of empires! What are you gonna do?"

That's really it: it's not some ancient wisdom from Plutarch or Kipling or even William F. Buckley, Jr. We don't see it used pre-2001 to describe the fate of the British or Russians/Soviets, for example. If this pithy phrase had existed in the 1980s-90s, one would think it would have been applied to the Soviets, but no such usage has been located. For that matter, it would have made a great title for Lady Butler's painting of the solitary horseman returning to Jalalabad from Kabul in 1842, but she had to settle for "The Remnants of an Army."

This is admittedly a tough one since I'm trying to prove a negative. I'll note that u/omid_2 posed a similar question based on a bit of preliminary research showing the phrase "graveyard of empires" is attested earlier but only in application to other places. See also this thorough answer on Afghanistan's history as an object of conquest written by u/Noble_Devil_Boruta which starts off by agreeing there's no direct evidence Afghanistan was called the "graveyard of empires" before 2001 and then (as I read it) explaining that such a reputation would not have been earned. This Politico article similarly argues that Afghanistan was really the "roadkill of empires." And there's a very similar argument here, also attributing the phrase to that 2001 article.

So, basically, Afghanistan hasn't been called the grave of empires except very recently, and that's because it hasn't really been perceived as the graveyard of empires.