In most cases, you're right that the motive is to effectively display content, and there are times when I allow it through. Obviously, the examples you present will require scripting to run.
However, I find it arrogant and unprofessional to present the visitor with a blank screen and no explanation of why scripting is so "critical" to the site's entire Web presence. The developer has picked a funny way to ask for the visitor's trust.
You've got to know your target audience. If it's the general population, it would be a courtesy (and the law, in some cases) to have a screenreader-accessible site. Read up on accessibility - there's a reason that the creators of Flash are trying (albeit with limited success, so far) to provide alternative text and captioning to what is essentially a multimedia programming language.
I have nothing against Flash or any scripting - I use it at work, where the users (students) can't turn it off. It has a place. I've used modeless dialog boxes, which are generally used for annoying ads on the Internet, but are really very nice for small standing reference boxes, when you're going through an IMI-format lesson.
I have the Flash plugin. I also have the NoScript plugin, which allows me to leave it (and all scripting) turned off most of the time. If that makes me a puritanical poseur, then fine. Hopefully, I'll be a puritanical poseur without a rootkit.
People carping from the sides of the Internet do bring about change. They're often the "computer person" that their friends and relatives turn to, to scrub jacked-up computers. I believe that the vocal minority is probably responsible for FireFox's growth to 20% market share, in the face of Microsoft's view that Internet Explorer is all we'll ever need.