Questions are occasionally protected when they start attracting unwanted input -- because the question was on the Hot Network Questions list, because it hit Reddit, because it's about a hot-button topic that everybody wants to weigh in on... Protection allows a community to prevent some stuff that they would otherwise have to clean up later on a small number of volatile questions. Currently you need 10 reputation earned on the local site to answer a protected question.
This proposal is to broaden the restriction to include comments. Currently, anybody with 50 reputation can comment, so people with the association bonus but no local reputation can't answer but can comment. That's kind of backwards; answers are first-class citizens, the stuff we want, and comments are meant to be disposable. So if people in this group can't even answer, it's counter-intuitive that they should be able to comment. This restriction should apply to comments on the question itself and on answers.
Further, questions that have gotten the kind of attention that leads to protection tend to attract more comments, sometimes quite voluminous. For all practical purposes only moderators can remove comments or relocate them to chat; the community doesn't have the tools to do this effectively.
Note that this dovetails nicely with the general encouragement to take comment discussions to chat -- users with an association bonus can use chat, so this is a little more incentive to go there to discuss the question. Perhaps the protection notice could even include a link to the site's main chat room. Participants aren't turned away but redirected.
Most questions are not protected; people can participate normally on the vast majority of the questions on a site. Protection is an exception, but when it's needed, there's usually a lot of action -- and in my experience on several sites, comments tend to be part of the problem. The number of valuable comments that would be lost -- that is, requests for clarification or suggested improvements that nobody in the local community can offer -- seems small. The number of...other...types of comments is much higher.