clone relies on hardware being designed and software written - this takes a lot of money, so you can't just count the final price of parts as the price.
Arduino is open sourced in hard and software which allows this cheap cloning to exist. It also helps a lot with software and docs, which makes it cheaper for them.
A competent engineer designing a devkit as simple as an arduino needs about 1 day of work. Give it a week to include debugging. Amortize that cost over a million units and engineering time comes out to less than one cent per board.