Since when did Apple "do AAC"? AAC is a standardized format that makes up part of MPEG-4, contributed to by dozens of companies and organizations. The patent licensing is handled by Via Licensing, not Apple. AAC has patent licensing fees too; over a dollar per device (albeit with a very low cap, IIRC).
, as well as because it is just a better format.
MPEG-4 AAC was the successor to MPEG-1 Layer 3 (MP3), by the same organization, so this is no surprise.
ALAC was -- for many years -- a proprietary FLAC-alike. There was no real reason to use it except for compatibility with Apple devices, as the two use nearly identical compression methods and the incompatibility is purely gratuitous.