Yes, that is the collateral damage inflicted by participating at the current ad model far to long. However, for sites who really want to change, this isn't a real problem. First of all, if you don't serve ads via "ad networks" but as part of your hostet content, I don't think the ads are getting blocked by default. Also, if a site with true content and regular readers has a proper ad model, they can just ask their readers to whitelist their site. If you don't just ask because you don't want to get your ads blocked, but at the same time can tell your readers why this won't be a problem for them, I think many would whitelist the site - if whitelisting is needed at all.