Well, it's more secure, and NOT because it's used less. even if some virus had infected say, firefox... It wouldn't be able to do much harm because nearly everyone who uses linux does NOT use a root/administrator account, which means that the virus can only do damage to files that are directly controlled by whatever account they infiltrated...
It generally runs faster than windows, due to various things, such as not having unused drivers to clog things up, and unnecessary background processes, unless you did something stupid and added them yourself...
It's much more customizable. Sure, you could replace explorer.exe with some other shell in windows, but many of the shells for windows are either incomplete, buggy, or simply don't provide as much customizability as most linux shells. There's just overall more options with linux.
Linux is easier to code for than windows, meaning that if you're smart enough to do a bit of coding, you can easily make small utilities for yourself quicker and easier than a windows user could.
In that same vein, shell scripting in linux is extremely powerful and useful. You can extract data from various applications' output with relative ease, and do all sorts of crazy things. Sure, it's possible to replicate most of that in windows, but it's much harder for the most part.
You can compile your kernel to only support what you actually need, meaning that your system won't have drivers you don't need clogging things and slowing it down. And linux has support for a lot of hardware that windows doesn't, thanks to the fact that it runs on so many different platforms.
Also, instead of being stuck running on x86 or x64 systems, you can use damn near any processor you want, so if you feel like making some really custom system, you can actually run linux on it.
I know many of these don't apply to the average computer user, but they ARE advantages of linux.