The problem is that many ads are ANNOYING. Get rid of popups. That includes floating elements that cover up the article content. Get rid of flash and any animation or sound. Stop popping up hover ads when I try to get my mouse cursor from the corner of the screen to some relevant link in the article (especially annoying when the hover ad then covers the fucking link and I have to click some miniscule close button to get the ad out of the way again).
I don't run adblock, but I do run Flashblock, and if someone had an extension that only disabled ads that screw up the page layout or are annoying, I'd gladly and happily run that too.