Even on Windows, it works fairly well with MingW. Most porting pain comes from bad package management.
Many POSIX-compatible libraries using autotools/libtool can be compiled on OS X without changes, and often MingW too. That isn't true for many other systems.
More importantly, when you do need to make a change, it's a simple edit of shell code and some pretty straight-forward makefile variables. It could just be unfamiliarity, but I've tried customizing the output of CMake for some specific situations and the complexity of the its makefiles is pretty prohibitive. Trying to change the CMake source files for someone unfamiliar with its "language" and variable name conventions is annoying and error-prone.
If I had my druthers here, I'd like a build tool that wasn't a layer atop GNU/Linux/Unix — and that's not to imply how autotools works here is at all bad or particularly wrong, it's just an approach that's a bear to port the tools — and have that (portable) build tool then generate the platform-specific build script, build procedure, build-whatever equivalent.
Conceptually: to move the existing builds from a procedural, interpreted approach into a higher-level and object-oriented approach.