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.
Not globally true. In West Africa, the term "one-stop" is often used to describe what in North America would be called a "non-stop" flight. The logic being that the flight only stops at its destination. I guess a "non-stop" flight would be one where you have to parachute out overhead the airport, but that term is almost never used. "Direct" is used to describe a flight on the same aircraft, even if there are interim stops or flight number changes.