I have seen on more than one occasion where new users get downvoted, questioned, flagged, etc. if the wording in the question is slightly off, there are "weird" parameters in the URL they linked to, the question seems lazy or too easy to find the answer for on Google, etc.
Are Stack Overflow moderators scaring away new users?
I like the ability to question the validity of posts etc., but perhaps in cases like these, the questioning should take place "behind closed doors" i.e. out of view of the new user; where only moderators or people of a certain reputation level can see the comments.
I totally understand the desire to KILL ALL SPAMMERS, put lazy people to work, etc.. But at the same time I have run into people who are so completely dumb, they don't know where to begin. Stack Overflow is more and more frequently becoming the top search result in Google, and as a result it's getting a lot more "noobs."
On the question screen, add a "moderation comments" box or "type" of comment, that essentially differentiates comments related to moderation so they are visible to users who have at least a certain reputation.
New users (users not logged in and users with limited reputation) won't see all the questioning / commentary, and it gives StackOverflow moderators the opportunity to discuss / research the right decision before either flagging the user to death or providing a helpful response (editing the users' question, adding comments with appropriate links to FAQ's, etc.).