There are a lot of different alternative Makefile generators and build systems out there:
- CMake
- Scons
- Waf
- Boost Build (aka BJam, C++)
Also available, but not stringently targeted on C/C++:
- Premake
- Ant (for Java)
- Rake (for Ruby)
- (Definitely more, I just don't know them all...)
But after listing these all, autotools have the great advantage of not requiring any other dependency for the end-user. A configure script is only generated once by the developer and does not require anything special on the user end, as it is a shell script. The tools listed above have to be installed before anyone can build your source and they even might have dependencies themselves.
