Largely for three reasons. But first I do have to point out that no system is impenetrable. Even Linux can be cracked.
Now, there are three primary reasons Linux is so secure:
1. It has a sane security model that can be extended and even overhauled as needed. Home users will be fine with the vanilla access control lists, but corporate users may like mandatory access control, such as Tomoyo or SELinux. The military actually mandates Linux has a working SELinux setup on their systems.
2. Linux users are, and I don't mean this as an insult to Windows or OS X users, the more competent computer users. The average Linux user knows how to keep their systems stable and secure better than the average Windows user, as many Linux distributions favor having users much more involved in the maintenance process. Many people think this is a shortcoming in Linux. I personally think it's better. One of the reasons, I think, Windows frequently fails is because it hides as much implementation as it can from the user. While it may make Windows "easy" it also means that Windows is impenetrable for the curious or the power user or for any do-it-yourself people who would like to fix and customize things.
3. Linux is open source. This is part of why there is a 1 and 2, but the third benefit comes from the fact that most Linux exploits are only 0-day exploits, as bugs are much easier for people to find. Someone encounters a bug, someone else finds the bug, someone else fixes the bug, and the kernel releases bug fixes very frequently. This means a particular exploit does not last long, making the lifetime of a virus very short.
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