Linux kernel? Uses its own automation. See also *BSD make, which is the basis for ports among other things (unless that's changed since last I looked); entirely in-make. Plan 9 and the userspace port uses mk, which is a slightly cleaned up variant of the BSD make.

Fact is, a makefile for building C code is typically smaller than the autoconf files required to get autotools to work on the same code. Most horrible makefiles are written by terrible build automation software (autotools being among the worst offenders here) or by people who don't understand the dependency graph model. A ten line Makefile that automated something repetitive is fantastically important, even if it is just writing down something in an executable fashion such that you don't have to remember it later. Almost every build automation tool out there either doesn't scale up (too simple) or is too hard for small work, or occasionally both, like Ant.

If I need to do something simple, a Makefile is only a very little bit more complex than a command line—I frequently crib the command I just ran to start off the Makefile. If I needed to do nontrivial logic in a Makefile and couldn't avoid it, I wouldn't use jam or tup or redo or SCons—I couldn't, because they're less useful than make! I would probably end up using Rake, which is the only build automation tool I've seen so far that isn't a make clone and can do implicit dependency generation.