I would not have any problem with a nice banner, clickable, possibly surrounded by a color that does not make me want to pull out my eyes with a fork after having 4 seisures and 2 strokes.
I do though have a problem, when a 3rd party tries to track everyone, and possibly without the publishers you're speaking of know anything about what's running on his site (they do not care, why should I?).
What I would prefer publishers to do: write something useful and meaningful, and make users come back because of your content. Be it a book, a fanfic, a blog with random thoughts, poetry, etc.
People seem to forget that web is about meaningful content.
This is how you attract users.
And some last lines while we're at it. Why is it always the question "if we [publishers] stop using ads, what'll we do"? I seriously do not care. I do not HAVE to care. Same goes for any user. It's his job to find a way (hint: meaningful content) to get revenue. He's the boss after all, right? ;)