Sorry to hear that you are disappointed. Fly the Line offers a raft of customisation options that allow you to customise your route generation to include only the airports you want to fly to.
When generating a schedule using a real-world airline, the primary source of routes comes directly from that airline's real-world schedules. Therefore, the airports included in the schedules will automatically be a suitable size for the aircraft types operated by that airline. The schedules can be customised from there via a multitude of 'Airline Parameter and Schedule' options that are available prior to generating the schedule.
Conversely, if you generate a schedule with a fictitious airline, or one not included in Fly the Line's database, Fly the Line will not have any real-world schedules to reference, and therefore, will generate routes based solely on the parameters set on the 'Airline Parameters and Schedules' page when creating the schedules. By default, these parameters are set up to allow the maximum number of airports to be available in the schedules; however, that does mean that many airports may be too small for larger aircraft to operate from. When generating the schedules, it is therefore important to consider the type of aircraft you intend to operate and set the Airline Parameters and Schedules to acceptable values.
For example, if you're flying a jet airliner, you'll likely want to have a Minimum Runway Length of around 7,000ft, although that will vary depending on the type of aircraft you intend to operate.
As for your other questions, Fly the Line has default Aircraft Profiles that should be suitable for most aircraft types of each category. If, however, you find that you often receive negative feedback for speeds, for example, flying too slow on approach, then "Min Landing Speed (IAS)" can be adjusted as required.
Although Fly the Line only simulates passenger operations, you can set the "Max Pax" value to 0 in the Aircraft Profile, and that will allow only cargo to be loaded onto the aircraft.
If you get stuck on any of the pages or would like further information on its features, there are tutorial options available at the bottom left of most pages that will point you in the right direction.
Hope that helps.
Mark - Just Flight