Questions are protected based on things you don't see, almost by definition. Spam and really poor (non-)answers get deleted and the rest is generally OK. Usually, they are also questions that attract a lot of attention so they will also have good answers, lots of votes, etc.
It does not prevent the question from staying there, (most) people from answering it, answers to be upvoted, etc. and is completely unrelated to the quality of the question or answers that are still visible. It just prevents unknown users from posting junk that has to be deleted.
I am not a moderator and have no particular insight in their decision process but I can see deleted answers and, in practice, one bad answer on a popular question seems to be enough to justify a protection (that's bad as in spammy or gibberish to the point of being deleted, not bad as in debatable or low in quality).