Here's a quick reference for the tools we've got for handling questions and when we should use them:
Downvote (Requires 125 reputation)
This question does not show research effort, it is unclear or not useful.
Close (Requires 3k reputation)
This question meets one of the close vote criteria, as LPMF has already described. More generally, if answering the question is likely to be harmful in some way then it should be closed (and there will be a close reason that reflects this).
Protect (Requires 15k reputation)
This question is likely to attract lots of views and newbies are adding "me too!", "thanks!" and possibly even spam non-answers. (I tend to do this if it's attracting "forum style" non-answers or a ton of low-quality "not really answers" as well, given the number of drive-by users we've got that do this sort of thing)
Flag
A question needs closing or deleting fast and/or you can't cast a close/delete vote on it. It is evil, weird, or in any way exceptional and deserving of moderator attention for any reason.