In an interview with Fast Company, O'Neill said that "what was interpreted as a policy that would give Evernote employees the opportunity to read users' notes, was actually a reference to using user data, with their permission, to help improve new features". It's becoming more common for companies like Evernote to imbue their software with machine learning technologies to better sift through data, recognize the patterns and habits of users, and display relevant content or perform certain actions based on what the software gleans.
If you're anxious about the content of your notes falling under the eyes of an employee or through a government request, you can always encrypt them so even employees can't read them, but it's still an off-putting practice for some people.
Evernote now says that while it is "excited" about the possibilities offered by machine learning, it is sorry for the breach of privacy implied by this clause.
There, you can uncheck the option to have the company collect your data.
This is due to Evernote needing to prevent fraud, illegal activities, and recognise threats, and that there is no way to block the company completely.