These popups are annoying but not harmful as long as you don't install their crap software. Most of them are just ads for crappy registry cleaner or antivirus software. Some may be an attempt to spread a virus.
I think y'all are right! I read the Spanish newspaper El Pais on-line. Don't ask me why, it is a progressive newspaper and it makes me mad as ****, but I keep on going back to it. Anyhow, the last couple of weeks I've had trouble with my internet security program not liking that website and declaring it "suspicious". But I ignored it, because I have been reading that paper for years. It was while on the El Pais website that I got that pop-up. Good bye, El Pais, this time I mean it!