Its really difficult to compare the two. Lots of Linux simplicity might be just very superficial, hidden in the rarely visited dark corners, whereas in Windows the complexity commonly is bit more upfront. Much of this stems from the fact that NT is just much more modern design overall, while Linux builds upon the ancient UNIX design. So when you look at Linux you might only see the relatively simple original UNIX there and then think Linux as simple. But in reality lot of the complexity rises from trying to cram in all the new features we expect these days into the old design, especially when in factor in the complexity in userland.

Second view on the matter (which is more hearsay than hard fact) is that with the relatively advanced kernel WinNT team had built they were running into critical performance issues. This probably was exacerbated by Windows more often running on weak PC hardware at a time when UNIX systems were heftier workstations and servers. These perf issues required them to make major compromises to the system to make it sellable.

Another more minor reason might be that WinNT was from the ground up designed to be both portable (at least to Alpha in additon to i386) and flexible enough to provide different userland interfaces (in addition to Windows, it also had POSIX and OS/2 interfaces), whereas Linux was very much i386 and POSIX only early on.

edit: oops, forgot one more thing: Windows offers an API for drivers whereas in Linux drivers are generally considered a part of the kernel itself and the APIs they use are not public. This design decision makes Windows API surface inherently larger.