Many a recipe or package instructs: 'cook uncovered' without stating a reason. As a general matter, is this to protect me from boilover, or does it have some more subtle purpose?
Simmering uncovered serves two purposes. The first is liquid reduction. Simmering with a lid on causes condensation on the inside of the lid that will drip back into the food. If you're trying to reduce the liquid, the steam needs to be able to evaporate away.
The second purpose is temperature regulation. With a lid on, the heat won't dissipate quickly enough and your food will eventually advance beyond a simmer and potentially throw off what you're making.