I realize they probably bring in more revenue, but they aren't very classy. When I posted this to Metafilter, I'm pretty sure a good many people quit playing the game because of them. Couldn't you just use banner ads?
There's lots of diffrent Ad methods. Personally, popups bother me least, because they are blocked. Therefor they are the worst to use, so people have to come up with more obtrusive methods to gather more money.
But if they bother you that much, you can simply play a diffrent level.
Where else would MD get money? I agree partly that banner ads would be nicer, but they would mess up how the sight looks constantly. The current ads just interrupt for a few seconds.