yeah your airline can become unwieldy once it grows in size and once you upgrade to larger plans you can zoom around aimlessly and make less money.
I found consciously using small planes to feed and layover big ticket cargo into determined hub cities, and then using your big carriers to do big dedicated intercontinental flights, makes some pretty sweet bank. The trick is to load up a plane with all passengers/cargo going to the same destination, as this gets you a 25% payment bonus.
I know that it's kind of a "non-game" but I really enjoy tweaking and optimising my supply routes to maximise profits. Its a fun distraction for desk/toilet/bus/bed