In light of recent events wherein vandals began burning mezuzot found on the doorways outside of people's houses, I am wondering if there is ever a reason to remove mezuzot to prevent their desecration. Meaning, if a person knows or suspects that a mezuzah in her home will be damaged either maliciously or by extreme weather (such as flooding) what is the proper thing to do, leave the mezuzah up or take it down temporarily?
While I am not a rabbi, the general rule is that you don't flat out ignore a mitzvah unless there is some actual danger involved. If it is the mezuzah you are worried about, there are -- as has already been mentioned -- ways to protect them.
You can get waterproof mezuzah cases in either metal or plastic. As a sofer, I don't recommend the aluminum ones for outdoor mezuzot because they conduct heat which damages the ink and sometimes the parchment itself. here is one such case (no commercial affiliation.)
As Rabbi Tzaddok and others have mentioned, you can build a mezuza niche into your door, but it seems like an unnecessary expense and trouble. If you do, they are customarily left partially exposed so people know they are there. Covering the mezuza entirely might be a problem of מראית עין