Although I consider Alexandre Duret-Lutz's Autotools Tutorial, mentioned in elmarco's answer, to be the very best available, you should also know about the Goat Book:
http://sourceware.org/autobook/
The versions of the tools it deals with are rather old, but it's a nice introduction and it's presented in a logical order. It's also more complete than the Tutorial. It is perhaps best used as supplementary reading after you've worked through the Tutorial.
UPDATE
There's also John Calcote's book, it was published around August 2010 and it's really good. I'm not sure whether the whole book is online at that link, but at least part of it is.