I think it is unfortunate that artifacts were stolen and/or destroyed during the war in Iraq. These items are an important documentation of Iraq's history and are very important to the Iraqi people. Unfortunately, this is not a new practice or is it confined to this country.
In a country during wartime, there are many people who are desperate to find a way to acquire money in any way they can - desperate times call for desperate measures. I think people will pilfer through the museums for anything they can sell to provide for themselves and their families. People worldwide have wishes to own unique pieces of art and are a willing market.
Enemies of a country wish to attack in any manner they can. If they can hurt the people they are attacking by taking articles that represent their history, they are attacking the emotional center of the country. This is a part of their identity.
There would be no way to protect all the important artifacts in a country. The safest way to retain as many of them as possible would be to not have them all in the same place. They should be housed in several areas across the country or maybe even internationally. The museums should be as secure as possibly to deter looters.
With luck and careful attention, hopefully many artifacts can safely survive the ravages of wartime from both internal and external forces..