He also says later in the post you can write your own configure with a bit of bourne shell. If you expect your software to be widely distributed, a custom build script is a pain for distributions as most of them are heavily relying on ./configure && make with the appropriate arguments. Distributions also rely on the ability to override certain flags, something easy to do with autotools and quite hard with plain Makefiles (compare ./configure CFLAGS=... and make CFLAGS=..., the former don't override upstream CFLAGS).

I don't object that many projects have convulated and dated autotools scripts notably because they don't age well. It's easy to accumulate a lot of crap.

Most projects don't get autotools because they don't know how to use plain Makefile. They do because autotools bring much more than that.