I have it set for my Safari but still get them. Emptied cache and histories many times but doesn't help. They only pop behind if you click a link to any of the stories on home page.
Yes. Email the editor and inform him pop-behind ads are annoying and intrusive. Also let him know you'll no longer be a subscriber to their paper or their site because of it.
Other than that you could try Camino, OmniWeb, or Firefox. Each of which offer more powerful ad blocking features than Safari.
Pop-ups that respond to user clicks and other actions are much harder to block, AFAIK.
The best way to get around them that I know of is to block the ad server's hostname.
You might try Pith Helmet or similar software, though.