The intrinsic problem with a rootkit is that it worms it's way deep into your operating system ; if you infected with one, there is no safe way to eliminate it from within the rooted operating system, because if your kernel is compromised, you can't trust anything it says about your files, etc.

Thus to eliminate a rootkit, you have to shut down the OS and manipulate the file system from another OS, and in such a case, it's probably less costly to simply reinstall the operating system rather than try and audit the existing system and repair any rooted components.

As @Cumulus007 points out, the incidence of a rootkit on a desktop-usage Linux system is very low. The odds are a little worse for a server-usage installation, but still very low.