Yes, it can; for no less than three reasons:
- Enlightened Tutor (like all other 'search your library' cards printed so far) does not target a specific card in your library, so protection doesn't play a role here.
- Protection from X only functions when a permanent is on the battlefield. (Though players can have protection from X as well.)
- Etched Champion's Metalcraft ability only works while it's on the battlefield, so it doesn't have protection to begin with.
(not 100% sure about the third one, actually)