Reminder to those who have forgotten, Penguin is not just all about links. Penguin is about spammy sites [insidesearch.blogspot.com], period.
Another reminder, Google's unnatural linking messages started months before Penguin, so conflating these with Penguin just makes the conversation that much more confusing. The only direct, semi-authorative mention of links being involved with Penguin is Matt Cutt's exchange way too many links [seroundtable.com] comment at SXSW.
Links, and their link to Penguin, was then reinforced by a respected person in the search field who found that sites that were affected by Penguin had poor backlink profiles. Not much rigor went into that analysis because duh, what did he expect? Spammy sites have spammy backlink proiles!
Correlation. Causation. Face. Palm.
And it spread. Like wildfire. Everybody forgot that Penguin was simply about sussing out spammy sites and it became only about links, not also about other factors. We have to look at our sites and practices very, very objectively and can't be in denial while doing so.