I don't quite think autotools were invented to replace Makefiles. Autoconf and friends _configure_ the build environment by discovering locations of dependencies, feature sets, available compilers and build tools and other build conditions. This information is then used to generate the appropriate Makefile.

Makefiles solve a different problem; which is of local build dependencies, looking for changes, packaging and suchlike.

CMake, as it happens, was written because Autotools were particularly ineffecient at the configuration problem. Make happens to be very efficient.