There's a distinction though. Acrobat, Java, and others all asked to be let into Firefox. They update silently after that but they initially asked permission. If Microsoft made a .Net Assistant plug-in I can't imagine people would be upset.
But using Windows update (which most expect to update "Windows" not your other programs) is, imho, considered sneaking it in.
This is the geek's way of looking at the world, where we are God Lord and Master of all bits on our computer.
The average user is not. They do not understand that the browser and the operating system are separate. For that matter, they don't understand that the browser is not the Internet or Google.
(If you've ever done technical support for a web application with non-technical end users you end up answering many, many fun questions such as "I signed up for your website at home -- can I also use it at school? My email address there is different.")
Asking users to make complex install/update/etc decisions is asking users to fail. They should be presented with sensible defaults and a minimum of fuss. Windows Update is quite sensible: "This comes turned on. Turn it off only if you understand what you're doing. As long as you keep it on, we'll keep you mostly covered." Installing ActiveX, Java, Adobe PDF Reader, and Flash by default is also very sensible, because otherwise many users will have "The Internet is broken!" experiences.
But using Windows update (which most expect to update "Windows" not your other programs) is, imho, considered sneaking it in.