Do you mean building on Windows? I'd rather avoid doing that, and just cross-compile from my linux box. So far I've managed to avoid it, and things have worked fairly well.
That's familiarity. autotools is a baroque answer to a problem that's just simply less screwy than imake was. :D More to the point, autotools is really only Linux/POSIX centric. It doesn't do well outside of that- and sadly, you DO have to deal with Windows for some things... ;) (We won't get into the fact that autotools is two kludges on top of ./configure that were done to compensate for ./configure and Makefile deficiencies...)