One thing you're missing is that the news media is largely event-driven. "Joe the Plumber" (and yes, the media "investigation" was idiotic) has been doing things - appearing at rallies, chasing the media, negotiating a recording contract, etc. Ayers are Wright aren't doing anything - Ayers is continuing at his job, and Wright hasn't talked to the press since I think late April. In that sort of situation, of course Wurzelbacher will get more coverage.
What, exactly, is new to say about Ayers and Wright? News media can report "Joe the Plumber attends campaign rally for McCain". They can't report "William Ayers goes to work again today" or "Jeremiah Wright walked around his house".
(And wasn't it ABC - that evil "mainstream media" - that turned up the "God Damn America" tape?)
As for the news media in general - Obama got a higher percentage of negative coverage than McCain over the summer IIRC, although he did get more coverage. McCain's certainly got more negatives recently, although given that his campaign is leaking like a sieve, he went 100% negative (at least for a while), and his running mate managed to beat Joe Biden in the say-something-dumb contest, completely even coverage was never going to happen.