No, it's not that other music programs work together, or anything like that. Fruity Loops uses exactly what it says in the title: loops. If you want to write music that has a natural tendency to loop, such as rap or techno, then sure, this is fine. If you want to write real music, though, why not just start out with a program that uses standard notation? This way, not only do you learn a program that lets you compose the music you have in your head, but also teaches you the universal language of music.
Also, @ Azmyth: ProTools sucks because it sounds like shit. Everything that comes out of it sounds over compressed and generic.