I also had the same problem .
Flash Builder 4.7
Mac OSX El Capitan
I also had the same issue. ㅠㅠ
I can change font for editor in FlashBuilder for windows os.
but, I can't change it for Mac Osx (El Capitan)
I think it's a Bug...
Is there someone you resolve this issue?
Same problem here. I don't know ADOBE is still care about Flash Builder??