I've had this "problem" for years and it's no more a problem since I decided to convert FLACs and other non-compatible audio files to ALAC (=Apple Lossless) or another iTunes compatible format using XLD (X Lossless Decoder), which is a very reliable and flexible audio converter - and a free software, too. To download, click the ".dmg"-file in the download section of this page:
http://tmkk.undo.jp/xld/index_e.html
Only thing a bit "tricky" (as mentioned above) is: all settings go via XLD's Preferences window, but once this is understood, no problem anymore.
I have it decode into a destination folder already inside my iTunes music files folder, but not into "Automatically add to iTunes", so files not yet completely decoded won't be added by iTunes. This is the one step you'll have to do by hand.
You can drop whole folders (including subfolders) onto XLD's icon to make it convert everything inside while keeping the folders' hierarchy intact.
BTW: it reads cue files, too (no matter if for MP3s, FLACs or Ape, etc...). With a cue file open, it can download tags and covers from internet databases, too and add them to the converted files...
I still don't understand why Apple doesn't simply support FLAC files, but I gave up on this.
BTW: I use an old version of "Vox" or an old application called "Cog" to play non-converted FLAC files on my Mac. They still work on Yosemite (with some minor limitations...) I don't like the new "Vox", and VLC doesn't seem to be very reliable in playing FLACs. "Cog can be addressed to a specific folder shown just beside its playlist, but the files have to be added manually from there. To me, there's no problem with that.
I'd greatly appreciate a new but simple FLAC player for Mac. Simplicity is the one thing that "Vox" has lost with its new version. You keep playing with options and forget about the music. Fatal mistake.