There's a difference. It was a matter of principle for a Web site (not) to use pop-up ads or ads in general. It would be highly inappropriate for a large and successful business to have (especially pop-up) ads in their product (unless ads was their business).
Another aspect of ads from the early 2000: they were individually made for particular places, rarely generating any controversy. For example, I used to be a moderator on a forum dedicated to ActionScript, and we had a sponsor, who, basically paid our hosting expenses, and that sponsor had a banner in the header of the forum advertising lessons in Web design / programming. The banner was designed to match the overall forum appearance, it didn't track anyone's browsing history, didn't collect cookies... it was simply a big and fancy button linking to the sponsor's Web site.
The problems really started with the "media buying" waterfalls, i.e. the automated ad delivery. Ad agencies automated their job by providing customers with (semi-, but increasingly fully-automatic) ways to design their ad campaigns. In order to make these campaigns at least somewhat effective, they needed to somehow automatically reproduce the situation similar to the one I described having in the ActionScript forum: they needed to find a good match between the audience and the ad, but they had to cut corners because of the automation and resort to the unsavory mechanisms of tracking users' behavior. The decrease in quality had to be compensated for by increase in quantity. And that's how we got here...