I feel I should play devil's advocate and point out that ads aren't necessarily intrusive, offensive, malware-laden, evil and harmful to a site's reputation. Many are, sure, but some sites are able to advertise tastefully, or at least harmlessly. For example Penny Arcade has a stated policy of only advertising games they've played and approve of, and thus their ads tend to stick more or less to what readers might want to see. Some lesser-known webcomics I read like to share advertisement with other similar webcomics, which is great for all of them. I go to Gamespot and see ads for the same kind of games I go there to read reviews of; sometimes they're terrible games I'm not interested in, but the content is appropriate and I can't complain. And while I don't doubt the horror stories of some ads spreading malware, well, all I can say is my pc has never caught anything while visiting reputable sites.
The point is that ads can be carefully chosen to have content matching what people visit the site for, such that they don't hurt the site, and maybe even advertise something you'd be interested to find out about; it can be a win for everyone. That being said.. I have difficulty imagining any ads with content appropriate to Dwarf Fortress. Toady could advertise mainstream games he approves of, except he doesn't play them, and he's hardly in Penny Arcade's position to review games prerelease (i.e. when they do the most advertising) even if he wanted to. Or he could share advertising with games similar to Dwarf Fortress.. er.. wait, what similar games?
So I'm not against Bay12 helping to support itself with advertising (in theory), I think ads can be a win-win if they're appropriate to the website, I just can't think what could possibly be appropriate ad content for Bay12.