Microsoft underestimated the inertia of the applications market. NT 3.51 was fine if you used it as a pure 32-bit operating system. You could even configure it without DOS compatibility. Few did.
Linux is another matter entirely, if your binaries run at all from one distribution release to the next you're doing well.
Linux binary compatibility is actually pretty good. As is glibc's an that of many other low level system libraries. The problem is only programs that depend on other random installed libraries that don't make any compatibility guarantees instead of shipping their own versions. That approach is also not going to lead to great future compatibility in Windows either. The only difference is that on Windows the base system labrary set is bigger while on Linux it is more limited to what you can't provide yourself.