Google engineers want to separate the useful websites from the spam websites ("content farms"). Unfortunately, no diagnosis system is perfect. They will make false-positive and false-negative errors. The article focuses on the false-positive errors: site owners who claim their websites have been wrongly classified as spam. In passing, the journalist also tells us that there are spam websites that have escaped the penalty. Google faces a trade-off: reducing false positives leads to more false negatives; and vice versa.
What's interesting about this is to figure out Google's incentive. The cost of each type of error is different; the level of public outcry in reaction to each type of error is different. It took years for search users to make enough noise for Google to implement this tweak; it took days for the false-positive victims to get mass-media coverage. Google has many constituents to please: search users, advertisers, site publishers, to name a few. It's a pretty complex web.