They called it Windows the same reason that they called Word Word and Office Office.
Marketting. You take easily recognizable terms, trademark them by applying them to products that are completely unrelated to their english definitions. It's a common way of doing things. Like calling a car "cougar" or "explorer".
At least that's what they want you to think.
All in all it's pretty stupid. Like in US Patents is shows the legal system's inability to deal with the fast-paced computer world. They should of never been awarded the trademarks.
Microsoft's new word proccessor: Word. Microsofts new office suite: Office. Microsoft's new windowed operating system: Windows.
It's like Ford going:
Fords new automobile: Auto.
Hell people were calling windows windows long before windows ever came out. Mac's GUI pre-dates Windows by several years, and they call those boxes windows. X Windows was out a year after Mac's released their first GUI-based OS and that even uses the term "windows" in the name to denote that it's for a GUI based interface.
That's why Lindows was able to keep it's name for so long before they changed it to Linspire. Lindows is obviously a trademark infrigment on Windows. It's the same name for the same product with one letter changed. However Microsoft could never realy sue them directly on those grounds because if they did it would be more then likely that they would win against Lindows, but get the trademark made null because it's a generic computer term for GUI systems that was in use well before Windows ever came out.
It wasn't until MS successfully sued Linspire in a different country with different standards was when Linspire decided to give up on it's "lets get rich by burning on Microsoft" sceme, and resort to their current "lets turn Linux into the software version of free AOL cdroms" angle of attack.
It's not like it's a big deal, though. It's old news. That's why it's not called "Windows" anymore, but Microsoft Windows 2003, or Windows XP. Always now with extra letters and numbers to show that it's a specificly trademarked term.