For early advertising-supported websites, banner ads were sufficient revenue generators, but eventually the prices paid for banner ad clickthroughs decreased and more effective advertisements were needed. Popup ads by their nature are difficult to ignore or overlook, making them more effective than static banner ads.
Popups have a much higher click rate then Web banner ads do, so sites use them to generate more money. Many people are annoyed by popups and there are many popup blockers available for download on the Internet.
List of free popup blockers: