I personally block Flash by default (mostly to stop audio ads), and I have no problem turning it back on when a site requires it.
I don't know what's happening to web development, but since this app fever developers are fighting for eye candy and LESS accessibility. Sometimes I see a page that fails to work without JS, open the source and see just JS code. Where is the content? Web apps are often times also walled gardens, and completely break the functionality of the browser (based on linking, rendering text & images and using the back button).
Now even simple websites completely disable access to content just to show some silly animation.
The move to "web-page-apps" is not about eye candy, it's about speed, responsiveness and yes, usability. About not trying to awkwardly force an app down the http/html way.
A broken website/app is simply broken: if things do not work as expected, that's not the fault of webapps per se or JavaScript - it's all doable and not a big deal anymore (the back button thing).
No, it is about following fads, just as web development has always done. Creating sites that are slower, less responsive, and offer terrible usability is clearly not done for reasons of speed, responsiveness and usability. Enhancing a page with javascript can increase responsiveness and usability. Replacing the page with javascript is moronic.