The Hummingbird Update did not penalize websites. However, it was an update that changed the way Google understands queries and text. Overall, it improved the way Google understands synonyms and search intent. This now makes it easier to rank higher with natural on-site content.
You can use this update to your advantage by placing keywords synonyms throughout the content of your website. This will not only build authority for your primary keywords but will also help you index for more long-tailed keywords as well.