At 1 rep, a user can post, i.e. ask a question or post an answer to a question. They must earn sufficient rep to be able to comment.
Users with the association bonus get 100 points added, so a new user can post and comment.
Protected questions prevent users with only the association bonus from posting. They have to earn sufficient rep on that site. However, they are still allowed to comment, and post answers as comments, defeating the purpose of protecting the question.
Should protected questions block commenting with only the association bonus?