The "auto protect" feature is pretty new. As part of the change, Stack Exchange has allowed users with sufficient reputation to remove that protection status, instead of it being a moderator-only function.
There's no problem in removing protected status if you have the reputation to do so (I believe it is 3500 for us, since we're still in beta), so long as you think it will be productive to do so, and aren't engaging in a "protecting war" (which isn't going to be the case if the question was automatically protected, rather than protected by another user or mod).
If you see another user protecting questions that you don't believe need it, or even a mod doing so, feel free to either flag for moderator attention (good) or post another thread here in meta (better).
Personally, I think the automatic threshold may be a bit too low, so I've gone ahead and removed the Protected status (for now; we'll monitor the question due to some of the low-quality/troll answers you mentioned).