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differences you are not accounting for:
- Linux needs a lot less external, untrusted, binary-only software.
- AppArmor and SeLinux are ready. Should desktop security become a problem we would see a hell of an isolation layer.
- Differences in kernels, compilers, libraries, etc, would make it much harder for malware to spread.
- Linux users are much more skilled
Yes, if linux had 80% of the user base, there would be more security problems. Probably a tenth of what Windows has right now.