Honestly, just use Cmake. It is far easier to make it work cross playform and better yet cross compile. There's no good reason to write a Makefile by hand and no large projects do it anyway
Also, the Linux kernel is pure GNU Make (no autotools, since that doesn't really make sense).
But yes those are platforms/OSes and not applications. Applications typically work on multiple Unix flavors and Windows, so something like cmake makes sense. Although honestly it's a shame that they made the same mistake as GNU make -- not paying enough attention to the programming language design and ending up with a crappy macro language.
While that is true, they have a lot of wrappers and pseudo-meta-programming that makes it very simple to add a module to the kernel. It's unlike any other "pure GNU make" project I've seen.
Yes, and it was incredibly flaky and awkward to use! And slow.
I think they are migrating or have migrated to a custom system now
It used so many tricky macros that it already was a custom system, just one that happened to be built on top of Make.
More specifically, Google's Bazel [0] is the most serious attempt I know of to replace CMake/autotools, but it only just began to support Windows [1] and requires the JDK. Say what you will about CMake, but it's a quick-and-easy MSI to install on Windows and has supported Windows for probably longer than I've been alive. Google's other open source build system, GYP [1a], supports Windows because it builds Chromium, but GYP might as well be undocumented. Unless you like spelunking into the Chromium source, GYP is a non-starter. (Props to the Node folks for actually doing this for Node and Node extensions.)
I haven't used Gradle [2], but I've heard more than a few times it's slow (warning: might be FUD)... and it also requires a JRE.
Ninja [3] is blazing fast, but it's specifically designed not to be used directly, but rather through a build system generator like CMake.
I'll be the first person to ditch CMake if a feasible alternative presents itself, but if you want to build a cross-platform, moderately-complicated C++ project today, especially one with dependencies on other libraries that use arbitrary build systems, I don't know of any such alternative.
[0]: https://bazel.build
[0a]: https://gyp.gsrc.io
[1]: https://docs.bazel.build/versions/master/windows.html
[2]: https://gradle.org
dpdk seems to be moving in that direction i.e. using meson.
I have particularly noticed the uptick in QMake usage in OSS projects lately, probably because it is so straightforward to use for the most common cases. I think it's not more popular than it is only because it's associated with Qt, and many people (wrongly) assume that it can only be used for Qt apps, or that it depends on Qt.