Maybe because Module::Build works out-of-the-box on Windows for pure-perl modules? ;-)
No need for nmake.exe, which, at times, can be hard to get into the environment. My own "auto-install" script actually handles Module::Build easier than regular makefiles simply because M::B-based modules will install on Windows. I can be reasonably sure that this is going to work on the hundreds of machines that may need it - now, and in the future.
I do create a dependancy on Module::Build. However, it, too, has a Build.PL script which works, so I can auto-install it before auto-installing the rest of the modules. In fact, it's tempting for me to actually create a Build.PL script and put it in Makefile.PL-based module distributions for internal distributing. If I need to auto-install any Makefile.PL-based modules, I may actually do that.
It really depends on what your environment is - if you've already gone through all the work for setting up nmake/compiler, or if you need XS-based modules, then you probably prefer Makefile.PL. If you're starting from scratch now, I found Build.PL way easier to call. It installs a bunch of stuff I don't care about (man pages, etc.), but I can live with that. Too bad we didn't have the best of both worlds, and everyone using that. ;-)