Serious question: Why THE FUCK are industrial controllers connected to the Internet still running Windows? What is going on here? Why did anyone ever think this was a good idea? Your customers may use Windows, but you don't code your site as a batch script ...
The only real reason I've heard comes down to cost and support. It's easy to develop software for Windows, easy to find developers, easy to support the operating system, easy (debatable) to use in an industrial environment. It's a known factor.
Always remember that people on the shop floor (or hydrocarbons refinery equally) aren't interested in maintaining a PC they don't understand, and their management aren't interested in maintaining a well-educated IT department. It's a simple cost/benefit equation, and so far the benefits have been completely ignored.
Likewise, vendors of control systems don't want to put the time and effort in to develop their IDE's, display tools etc for a Unix variant. System integrators (ICS programmers and configurators)... well, we'd be cool with a Linux-based control system, if it worked well.
That's why you see Windows in industrial control environments. Couple this with the extremely conservative nature of industry, and you have a huge, glaring problem. We (ICS engineers) know it's a problem, clients are starting to realise it's a problem, but the wheels move slowly.
At least Stuxnet has made the wider industrial community aware of just how deep the shit is. Now begins the slow process of crawling back out of it.