In addition to protecting questions to avoid spam or "thanks!" answers, we often protect questions that attract negative, irrelevant, or otherwise low-quality answers.
I also tend to start removing comments-that-are-answers once there are a large number of them, particularly if they're descending into negative tone. This is pretty clearly covered in the Help page about commenting (excerpts below):
Comments are not recommended for any of the following:
Answering a question or providing an alternate solution to an existing answer; instead, post an actual answer (or edit to expand an existing one);
Secondary discussion or debating a controversial point; please use chat instead;
But when a passionate new user feels they have good information to share encounters a protected question, what's the solution?
Should comments be moderated more permissively than usual on protected questions, in order to allow users to "answer" even though they don't have sufficient reputation to Answer?