From the Wired article:
If they're not replacing advertisements with their own, and they're not inserting their own additional advertising into the pages, and the advertising is more targeted, then wouldn't this be a good thing for websites owners and a bag thing for Charter's subscribers?
Even in a worse case scenario, webmasters could come up with a way to circumvent their "enhancements". We did it with Gator and countless toolbar schemes. I don't think the ISPs could stop us either.