Then their site doesn't get return visitors and starts dying, just like Flash is.
Most JS use is sparing and lightweight and more about interaction than action/animation. Most Flash use is heavy-handed, ham-fisted, and overbearing, done more for cosmetic effect than additional function. Is this a part of the technology? No, but it certainly is nurtured by the differences between the development environments — Flash is still sold as an animation studio! What's more, JS gets to manipulate the DOM directly, giving it a much nicer relationship with the typical web experience than Flash, which is effectively a replacement for the DOM.
Have you used Twitter or Facebook on resource constrained machines? Even on latest nightly builds of Chromium it's painful on my Dell Mini netbook.
The point is that you can use Javascript do just about everything you can do in Flash. And Adobe CS6 will almost certainly contain some tools to help you use your existing Flash assets in a pure JS+HTML+CSS environment. So the animation studio for Javascript doesn't exist yet, but we're talking about the near future where it will and it will be just as obnoxious as Flash (but much harder to block from consuming CPU.)
Imagine what Gmail would be like if they went overboard with CSS.
You might be overestimating the differences between Flash and JS here -- especially when you add HTML5 into the mix. What's to stop a skilled JS dev from playing <audio> when the user hits a page, burning processors with a few autoplaying <videos>, after forcing the user to sit through an interminable, animated <js/css3/svg> 'loading' screen? At that point, it's up to our own good tastes to decide how to wield that kind of power.