It's really just lazy writing. The WTC was attacked in 1993 so it was well known to be a target. Plus you had the OKC bombing a few years later which just confirmed that government structures were targets. Flying planes into stuff wasn't a new idea either; the earliest cruise missiles were basically jets with some remote controls added to them and even suicide-pilots were an old idea by then (kamikaze's in WW2.) And the idea of a plane crashing into the WTC wasn't even that novel before the 1993 attack. There were numerous experts criticizing the possibility of a jet accidentally crashing into them when approaching the nearby airport, so much so they eventually tweaked the flight-lanes around Manhattan to limit the chance of an airliner hitting them in bad fog.

So to have a plot about some jerk remotely flying a jet into a famous skyscraper that had already been attacked once before isn't all that surprising.