There are many possible answers to that.

First of all, at Southwest (which is the airline that prompted this thread), they fly point-to-point-to-point (not hub-and-spoke like most other airlines), and they might fly a route simply because they need to get from point B to point C, and selling tickets is better than flying an empty positioning flight.

Second, once again at Southwest, they've chosen to fly on one plane type. They can't size to a smaller plane if the market is smaller. But they may not want to give up a market just because it's not perfect for their one and only plane size.

Now, something that can apply to many airlines: Some routes to small airports are subsidized by local forces.

Now, something that can apply only to multi-class airlines (and thus not Southwest): If the route fills up first class with paying passengers, who they hell cares if half of the back is empty?

Now, something that can apply to all airlines: If the route fills up half the plane with people who (because of booking late or any other reason) pay the much higher fully refundable (business) fares, that can more profitable than a plane that's 100% full but all at discount prices.

Now, something that can apply to certain bigger plane types especially: Some routes are paid for by cargo (this is why American flew big planes to small Caribbean destinations for years, for example).

And on, and on, and on. Ie, if you're not the in airline business, you may not be aware of how complex the profitability of a given route can be, and it's far from being as simple as whether every seat is sold out or not.