Most of the GNU software catalogue has historically been supported on nonfree platforms. Nothing to do with Linux here, it's not part of the equation.
None of this consideration is really concerning free software or proprietary software specifically. It's simply looking at cross-platform capability. If you need to develop cross-platform software of either sort, it's not typical to be able to ignore Windows. It's ~90% of the market. Similar considerations for other markets like smartphones.
None of that is reflective of my personal preferences, simply stating the requirements which drive the build system considerations of many projects. The GNU Autotools are unsuitable for the vast majority of current systems in existence, and that means selecting it for its portability is nowadays often not a possibility because their choice to not support common platforms makes it untenable.
