Flash wasn’t an open standard and was a pretty poor standard at that. The main reason it wasn’t supported on the iPhone was that it was never designed to be used by touch devices.
The headphone jack is open, widely used, its design has been validated over decades of use, and is widespread.
Just yesterday I was the only person at an event who was able to play some custom music our family wanted to hear because my iPhone 6 was the only phone with a headphone jack that could then drive music to the DJ’s professional setup.