Answer:
Trying to compare Rockbox and Linux is like trying to compare apples and oranges (unless you are talking specifically about iPodLinux or something similar).
On the one hand, you have Rockbox. It's meant for MP3 players. It has very specific functions that it was designed to do: play music, and maybe run the occasional game.
On the other hand, you have Linux. It's a fully-functional operating system. It has many functions that are not limited to controlling an MP3 player. It can be used to serve websites, design graphics, make films, write documents, build programs...you get the idea. From personal experience rockbox is easier to install and has a lesser chance of bricking an iPod. With Linux its pretty easy to brick an iPod installing it.