Market analysis, historic data, economic data, etc.
Tons of data to factor in: Are customers willing to pay more to have a non-stop offer compared to current 1-stop connection are the? Are there tons of companies needing these flights and are willing to pay top dollar (Air France has for instance flights to parts of Africa that see plenty of oil and gas employees)? Etc.
Or you could just throw a dart at a map. I would imagine that's how QR ended up with a handful of destinations like Cardiff.