Autoconf requires GNU m4 at build time and POSIX sh at runtime. It also requires all the standard UNIX command-line tools you would run from the shell.
Automake requires Perl at build time and Make (preferably GNU Make) at build time.
A stock Windows system doesn't have these tools. Cygwin and MinGW/MSYS provide these, but you're using stuff which is non-standard for the platform and which if you need to integrate with other libraries and tools, end up being incompatible.
If you want to use MSVC, the Autoconf/Automake support is poor. Generating output other than Makefiles is possible, but limited and quite the undertaking.
CMake supports all these other use cases out of the box. Which is why it gets used. It works on every platform, and with every compiler, build system and IDE of note.
I don't know, I guess each project fails in a different way (my experience was mostly with libcurl before it came with cmake support), but IME projects which come with a Makefile or use autoconf don't care about non-UNIX-y operating systems, while (again: IME) a CMakeLists.txt file is often a sign that the project will also build on Windows with MSVC.
