GUI is easier for a total beginner. JASS is easier for someone who has some previous programming skill. If you are not particularly good at programming then I would advise against JASS, although it is fairly easy so you may as well give it a shot.
Mastering the basics is all up to the individual. It might take someone a day or a few months, and once again depends mostly on whether you have any programming background and thus whether you need to be (re)taught concepts such as strings, arrays, functions, etc.
As for protection, it's because all map code is stored as JASS but is also stored as GUI if it was created specifically in GUI. Since deleting the (useless ingame) GUI-only files reduces map size, people like to include it in map optimizers.
