There was a recent change to the system that prevents the protecting of questions by 15K users unless additional criteria are met. From bluefeet's answer on Meta Stack Exchange (emphasis added):
15k users will still be able to protect but in order to do so the question must have at least one answer by a new user aka a user with < 10 rep on the site (which is the required rep limit to answer protected questions). [emphasis added]
If the question does not have an answer meeting this requirement, then the protect option will not be available. This should minimize some of the protecting of questions that do not need it.
The Protect Questions privilege page now also reflects this (emphasis added):
Any question at least a day old can be protected and unprotected by users that have the privilege, provided the question has received at least one answer from a user with less than 10 reputation (such users would then be prevented from posting further answers after the question is protected).