Actually it is iTunes fault, they were late to the digital music game and to capture their market share, they relied upon marketing the apple name and making it so if you bought into the iPod, you had to buy their music and vice versa.
Well the vice versa part is right but you can put plain old MP3 on an Ipod....
Heres the thing regardless of how any of us feel about Itunes they are by far the biggest player in the game when for your software company it's an easy fix to work with them. From what I understand it's a couple of hours of coding to get any common software to play M4A.
Personally I don't mind taking the extra step to convert generally unless you are buying a collection off Itunes it's a less than a minute process