Exactly. There was a time when the idea of users accepting/rejecting cookies on a per-site basis seemed plausible (though it might be annoying for the user), but those days seem long gone. Cookies are on by default and my guess is few users change those settings. DNT might be viewed as another attempt, however futile it may seem, at giving users some choice.
It's true a good portion of the web still works well without Javascript. This seems like a good thing as Javascript can be a mixed blessing. Enabling it comes with both benefits and risks. Like cookies, a user could selectively choose which scripts to allow, one at a time (remember the embedded Java applet days?), but this can quickly become more trouble than it's worth.
Perhaps a difference of JS from cookies is that with Javascript the user might sometimes see what the actual benefits are and they might be more enticing than those of cookies, e.g., "To see this cool doodad, you need to enable Javascript." It is very clear what the benefit will be: the doodad.
Contrast this with "To use this site you must have cookies enabled." Terms like "provide a better user experience" might be used to describe the need to enable cookies. But the specifics are usually absent.
If all websites were reasonable, and no one abused their ability to manipulate and track end users, things like DNT would probably not be necessary. But we know that's not the case.
