In the film, it is assumed (by the Nazis, anyway) that the army possessing the Ark will be able to control its power and thus use it as an infallible weapon. As the film unfolds, it is revealed that the Ark has a greater will than the Third Reich, and instead of the Nazis controlling the Ark, the Ark controls them.

It's actually kinda ironic, because a very similar thing happened in the Bible. Just prior to Israel's monarchic age, the Hebrew army was engaged in constant skirmishes against the Philistines, and on one occasion, in an attempt to tilt the scales in their favor, they took the Ark with them into battle, thinking it would ensure victory. In fact, nothing of the sort happened. Israel lost the battle, the Philistines took possession of the Ark, and Israel didn't get it back until years later. The entire affair ended up costing many, many lives.

(Just to pre-emptively clarify, I'm not trying to draw any parallels between the Jews and the Nazis...only between the mistaken assumptions that the Ark of the Covenant can be controlled by an army, and the tragedy that such misconception begets.)