Questions can be protected to prevent new users from answering them.
The resulting banner reads in part:
This question is protected to prevent "thanks!", "me too!", or spam answers by new users.
On Skeptics.SE, we do not have any problems with people posting "thanks!" and "me too!" answers. Spam is only a minor problem, and is not targeted at particular questions, so questions aren't protected for that reason.
Instead, looking at the protected questions (here is a superset query), they tend to be protected because they are on notorious issues that attract drive-by posters of very low-quality answers or non-answers. After about three of those, an automated process, or a frustrated mod, will go ahead protect the question.
The text should be updated - on Skeptics.SE site at the very least - to say:
This question is protected to prevent low-quality answers by new users.