The problem is not advertising, but rather obtrusive pop ups, and JavaScript tracking, and flashy banners that are often crude and offensive.
Apple is blocking these things, which are only a subset of ads.
There are plenty of ways to advertise that get through these blocks; for example Daring Fireball has basically paid commercials in the RSS feed. Sometimes they are a commentary from John Gruber saying “I’ve used this, you should too,” or sometimes it is just a direct message from the advertiser addressing the reader directly.
The BoingBoing Store is probably another stab at this, too. Same thing with advertorials.
My point is that there are ways to get around this. I buy tons of stuff as a result of things I read on the net, and nothing from banner ads. How can publishers move away from the robot automata, and cultivate a more curatorial relationship with advertisers?