Playing devil's advocate: since the operating system mostly abstracts the underlying hardware, when programming with a high-level language, an IBM mainframe running Linux and a MIPS router running Linux are both closer to an AMD64 desktop running Linux than the same AMD64 desktop running Windows. And Windows is a particularly annoying case, since its native API is so different from the Linux native API (and details leak even when using API wrappers, for instance removing a recently-created file can fail on Windows because some other process like an antivirus grabbed a handle to it).

But yes, I agree that a nontrivial fraction of the objections to making software run on Windows (or Mac) is for ideological reasons.