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They used to charge very hefty licensing fees ($10 per connector at one point!). I think (but I'm not sure) that this has now stopped but they still restrict what 3rd party manufacturers can make, for instance USB-C to lightning could only officially be made by Apple.
Given that Apple are adopting USB C on their ipads I imagine it will flow through to the phones at some point.
Apple are actually one of companies that hold a board position at the organisation that developed USB C. Quite why they are still releasing products with lightning I don't know.