They don't have the man power to stray far from their focused feature set. Just look at the mess that iOS 8.0 is. I don't know if they are not willing to hire more capable people or if they just don't care as long as the money pours in (that could bite them in the long term though).
FLAC is a niche feature and those features are usually only supported if someone at Apple has a personal interest in supporting it and if it doesn't get vetoed by the power that be.
In the case of FLAC it might even have been the latter as you could describe FLAC (not entirely correct) as the codec that let's you digitize your CDs losslessly. That view would put it in competition with iTunes (320kps AAC/MP3 ought to be enough for anybody?) and additionally, if you are a true Apple follower, you don't have a CD drive anymore anyway.