Even with all the GNU tools available there are still a lot of system-specific things that you may need to know: supported C version, supported C++ version, how to invoke the compiler, correct compiler flags for warnings / desired C or C++ version / etc, where to install things, how to install them and set the right owner and permissions and many many more. Autotools (and cmake) can figure all of that out for you. If you operate in a monoculture and, for example, only deal with a single Linux distribution on a single architecture most or all of this may not be relevant for you. But if you target a more diverse set of environments it can save you a lot of headaches.