The costs of annoying advertising

A study in CACM, "The effects of online advertising", has data on what many have argued for some time, that pop-up and pop-under ads annoy and repel users:

Pop-ups were [rated] 24% more intrusive than in-line ads and pop-unders were 33.1% more intrusive than in-line ads.

Subjects who were not exposed to ads reported they were 11% more likely to return or recommend the site to others than those who were exposed to ads.

Subjects exposed to in-line ads remembered 3.4% more of the material in the site than those exposed to pop-ups.

Designers should realize the magnitude of ill effects caused by advertising ... Reducing the likelihood of a person's return by 11% might be a cost that is too great for a site host to bear.

I wonder if websites that continue to annoy with pop-ups and pop-unders are only measuring short-term gains (e.g. clicks on the pop-up ad) and not long-term costs (e.g. loss in retention, higher abandon rate, lower return rate).