How can I add support for .flac files in SoX?
Keeping it simple. 

Removing it using brew like so :

brew remove sox


Then installing it again with specific options, like so, did the trick for me:

brew install sox --with-lame --with-flac --with-libvorbis


You may want to remove the --with-lame option if you won't be using MP3s, or the --with-libvorbis if you won't be using OGG.

I hope this helps someone.