They ship the phones with a small adapter that goes from micro USB to lightning. You're allowed a proprietary port into the phone as long as you provide the adapter for free.
http://www.apple.com/shop/product/MD820AM/A/lightning-to-mic...
$20 to buy in the US. Sure it cost $.10 to make.
http://www.righto.com/2014/05/a-look-inside-ipad-chargers-pr...
Better components, better design, better safety, and better assembly. Plus then you have to package and ship the things.
People complain about Apple selling $20 accessories, then turn around and complain about working conditions in Apple's suppliers like Foxconn (despite Apple doing far better on that front than their competitors).