There's two areas where Microsoft have at least some advantage over Apple:

1. The NT kernel has a very sophisticated security model, and in the past few years MS have actually started to take advantage of it rather than shipping with a promiscuous default policy. Darwin's security mechanism is less unified, though the default Unix-y policies have been an advantage for a long time.

2. The secure lifecycle effort. MS have really gotten very serious about thinking about security all the time. They still have decades of cruft to clean up, but ... so does Apple.