Autotools looks like a great idea: try to compile some programs and see if it works to learn the specifics of your environment. Yet I share the feeling from Julia that I hope to never have to learn how it works.
Nobody else knows how it works, which is why every configure script checks for a working fortran compiler. that is also why you can never be sure things like cross compiling work even though it can.
i use cmake - not a great system but at least it isn't hard and it always works. I've heard good things about a few others as well. There is no reason to use autotools.
My configure scripts never checked for a FORTRAN compiler. I'm not going to claim that using autotools is a pleasant experience, but it's not that bad, and it's very well documented.
