They get paid extra per click.
The art of banners in whatever form (integrated, popup, popunder, nag) is an exquisite one ine which ever inventive webmasters come up with more and better ways to screw their customers and visitors.
Having a high display/click ratio is a good way of attracting advertisers. Failing that, mass volume should put food on your table.
Well, not really, but hey it is a reeeeeaaally nice idea, because people just keep coming back to virus infected sites riddled with popups right?