They are automatic.
The reason it's not working is because the game only goes through the routes to check for flights that need to be scheduled every 10 minutes (so 06:00, 06:10, 06:20... etc). If you have more than 1 route assigned to a single aircraft, you have to make sure the 2nd route departs after that 10 minute mark. For example:
Route 1: IND-JFK-ATL, ends at 13:51
Route 2: ATL-JFK-IND [Must depart at or after 14:00]
The other thing you can do is simply make one long route, IND-JFK-ATL-JFK-IND and that will have no issues.
Probably need to make that more clear, either in the game guide or elsewhere.
The reason it's not working is because the game only goes through the routes to check for flights that need to be scheduled every 10 minutes (so 06:00, 06:10, 06:20... etc). If you have more than 1 route assigned to a single aircraft, you have to make sure the 2nd route departs after that 10 minute mark. For example:
Route 1: IND-JFK-ATL, ends at 13:51
Route 2: ATL-JFK-IND [Must depart at or after 14:00]
The other thing you can do is simply make one long route, IND-JFK-ATL-JFK-IND and that will have no issues.
Probably need to make that more clear, either in the game guide or elsewhere.
I am the developer of Airline Enterprise