There are several reasons why you may not want to implement the GNU Build System yourself (read: write a configure script and Makefiles yourself).
The GNU Autotools take all this burden off your back and provide:
Yet there also exist reasons why you may want NOT to use the Autotools... For instance you may be already using (or used to) another incompatible build system. Autotools will only be useful if you do accept the concepts of the GNU Build System. People who have their own idea of how a build system should work will feel frustrated by the Autotools.