The way I see it, they serve three purposes:
1 - They make the engine bay look all 'neat and tidy'.. hiding wires, tubes, hoses, etc..
2 - They keep people who might otherwise want to poke around, tinker, etc.. under the hood from getting to things they probably shouldn't. A lot of people know just enough to make matters worse.
3 - They can keep things from falling down into some of the tight spaces in the engine that they cover.
My Fusion doesn't have one, so it's not even an issue. My Altima has one, and I leave it on. I see no reason to remove it most of the time.