The cost of potentially blocked by ad blockers is finite (A percentage of total revenue), but the cost of ad-fraud is not bounded.
Isn't the solution to that problem a flat rate fee (similar to how advertisements on tv, newspapers and magazines work)?
Instead of a pay-per-click it could be a simple $X dollars and your ad will be visible for Y days/weeks.
The current solution is effectively a flat rate as far as an ad campaign is concerned: impressions/$
Needless to say, this could be inconvenient for the adwords-make-me-five-bucks-a-month scale sites. It'd work out OK for the New York Times-es of the world though.
But even with the added complexity of regularly pulling in the public suffix list, the problems keep going: e.g., facebook.com's scripts are all served from static.xx.fbcdn.net.