This is all so true -- but the same can be said for any method of tracking internet traffic. Think of the Alexa toolbar, or the new Compete toolbar (completely biased). This particular ramification will be more widespread, as the big traffic monitors like HitWise and ComScore who publish industry-standard numbers will be affected. So businesses that rely on those numbers should account for the skew (though, 10 years ago trend seekers relied solely on newspaper and magazine publishing stats to come up with numbers... yikes!). However, I find it hard to believe the article's report that "researchers found that 31 percent of U.S. Internet users erased their first-party cookies over the course of the month." Does 1/3 of the general public even know how a cookie works, never mind how to erase them?
Side note -- the person with all the traffic data? Google. Making Analytics free has created such a huge install base, they have an amazing amount of traffic data. Scary what they could figure out.