What is the rationale behind very short distance flights?
Because air travel is the best option in those places. 

The shortest commercial route in the world is between Westray and Papa Westray in the Orkney Islands, a distance of 1.7 miles. 

If you see the list of short routes, almost all of them are between islands. That instantly rules out buses and the like unless a bridge is built, which in most cases is not commercially viable. One can use a boat or ferry, but in most cases, the sea may not be deep enough or calm enough.