If you've already shot yourself in the foot, why not also shoot yourself in the face?
New keyboard etc etc
:)
Because if you write your own Makefile instead of using automake, you'll get shot in the face by a distro package maintainer when you forget to obey DESTDIR, CC, CFLAGS, etc. like every packaging tool expects to use.
I don't use autoconf myself. If I did, I'd definitely copy it from an existing project.