Are you kidding? Porting tools to other platforms is the main selling point of autotools. Why do you think it goes to such pains to avoid bash-isms in its output, sticking to raw POSIX shell code, even to the point of avoiding functions and loops? This is specifically to support weird esoteric * -nixes.
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.