This and only this.Simple: money
Apple gets royalties for every single device that hooks up through the lightning port. And they weren't making any money with the 3.5mm jack. It's the same reason they haven't gone with wireless charging yet, even though they want you to believe wireless is the future. They'll do wireless charging when they have their own proprietary tech in place. And only then.
If courage is another word for profit, then yeah, it was umm, courage.