Linux is capable of running IPv6, IPSec and making use of smartcards and similar security controls. These will...
indeed protect user identity and the integrity of some transactions and system communications. These controls alone, however, do not explain security differences between platforms.
Platform security depends on the:
- the robustness of the basic operating system
- the operating system configuration (especially its default state)
- the applications running on it
Thus far, compared to Windows, Linux has been more secure because its base operating system is robust and secure, most distributions are highly configurable and capable of being hardened (see tools like Bastille Linux) and their default configurations are usually secure.
Dig Deeper on Linux system security best practices
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