I agree with Lori. The pack cover is no protection at all for the pack contents if, for example, you slip and fall during a stream ford. Nor does it protect the pack contents from a long soaking rain that runs down between your back and your pack.

Note that stuff sacks are not waterproof even if made of waterproof material--the closure lets water in. You need a dry bag closure. Be sure to test dry bags in the bathtub every year.

I do use a lightweight (cuben fiber, 1 oz.) pack cover because my pack is my pillow, so I want the front side (confusingly, that's the side away from your back--the front as you pack and unpack) dry so it won't wet my sleeping bag while I sleep. However, I use dry bags to keep my insulating garments dry inside the pack. It's kind of a tossup whether you use dry bags or a waterproof pack liner (make sure your closure is waterproof), but definitely use one or the other!