The organic nature of it. I think in the long term, Linux is a good bet security-wise. One major advantage is that we're willing to break backwards compatibility, whereas purely commercial OS's cannot do so as easily. For example, when a.out got tossed in favour of elf, lots of people complained, but it's the standard now. Linux is infinitely malleable, so it can become what people need it to become.
Someone has to know the hardening tool exists, how to use it, and so on.
That won't happen, because vendors and users put usability above security. Until users demand security from vendors, it won't happen. Until the attitudes change, we'll always be behind the 8-ball. The computer industry is a lot like the old car industry, with death-trap cars, until Ralph Nader came along and kicked some butt. Sue the companies they work for.