i think there are two big problems with popups...
1. the intrusive nature of them. when you are watching your favourite reality tv show, it's not like the commercial opens up right overtop of the show and you have to scroll over to the X in the corner and close it, only to find by the time you've moved over there the window has relocated itself onto the head of one of the characters and now you have no clue what is going on in the show and can't close the window...
2. webmasters are not targeting advertisements very well. the problem is, you're still somewhat local on television, whereas online you can't exactly say you only want american viewing audiences for your ads, etc. but when I'm viewing say a web site for song lyrics. why not give me ads where i can buy cd's or sign up for a columbia house membership or something. i don't need to win $500, i don't want to gamble in a casino, and i'm perfectly fine with the figure of my body thankyouverymuch.
this is sometimes due to advertisers not giving webmasters a choice of what ads they show, but targeted ads are effective ads. random ads, well, if you don't make any money it's not hard to wonder why...
with the pop up blockers though i think it's a classic case of the annoying few ruining something for the masses. so say some web site has 30 popups that come up and every time you close a popup window you get 3 more. and some are pornographic or otherwise offensive to your viewing audience. this is what makes people want to dowload these programs...so why not sue the webmasters that load their sites with popups? to the point of giving me the illegal operation box because there are too many windows and too many scripts telling me i need an x10 camera, go on a diet, or shock the monkey and win 20 dollars.
my $0.02