That is probably because most people outside the airline and travel industry habitually use "direct" synonymously with "non-stop". Having "direct" mean what it means in airline jargon is the source of this confusion, and probably leaves some passengers disappointed or angry that their "direct" flight involved a stop and a connection that they missed.
True. Very true, in fact.
But, our Reservations Sales Agents took a lot of calls from travel agents. So, there really wasn't any wiggle room when it came to terminology.