Yes! You can fly any aircraft in your flight simulation hangar from day one, but performance values and the overall Fly the Line experience are tailored to typical short-haul airliners, whether propeller-driven or jet. You could use, for example, the Just Flight RJ Professional as a City Hopper and the Black Square King Air as a charter. It's also fine to use long-haul aircraft too but your routes will be restricted to a max of 6 hours. 

Smaller aircraft (like the Just Flight PA-28R Arrow III and Black Square - Piston Duke) can be used for Wings of Wealth missions.