I'm not a fan of Windows but Stuxnet didn't happen because of Windows. Iran decided to spin up a nuclear program and Israel and the US had concerns and wanted to stop it. They had the resources to develop something tailored for this unique situation, which included windows, Siemens PLCs (IIRC), Centrifuges etc. and developed the malware based on their target. Even if their target used a different stack, they'd find a way to achieve the same result.
It's all about price. Attacking Linux will be harder, thus more expensive.
You make it sound easy, if that was the case they'd launch one attack every few months or so. This stuff is expensive, and making it 100x harder means 100x less attacks before the budget runs out.
