The key is balance. Advertisers forgot that. They took the short-view and went with increasingly intrusive and annoying adverts. They broke the balance in their favour, so we broke it in ours with filtering tools. It just so happens that it's easier to block every advert on the entire Internet than to be selective about it. And here we are.
So true. I get a dead tree newspaper and a few journals. The ads in these publications support them and don't annoy me at all. Sometimes I even learn something useful from an advertisement. I'm used to it. If ads in online journals didn't really annoy me, I'd never have bothered to figure out how to block them.
If Ars wants us to view ads to support their content, make it look and act like an ad in Science or Nature, seen but not detracting from the content. Show me ads as text boxes or non-animated gif/jpeg/png that stay in one place on the page.
Don't serve ads from any domain that serves blinking, animated, noisy, moving, flash, or most especially deceptive adds. Any advertiser that delivers deceptive ads WILL be blocked at the firewall. Adblock/Noscript takes care of the rest.
Really, Ars, we were fine with adverstiment supported publications for a long time. Poisoning that covenant was your own making. Now, it's just easier to block 'em all. So, if you want our eyeballs on your ads again, find another way to deliver ads so unobtrusively that maybe people won't bother adjusting their filters.