It's easy enough to buy waterproof covers for your panniers, or even line the inside compartment with a garbage bag if you're on a budget.

With that said I paid extra for waterproof panniers (Ortlieb vs Axiom) and I feel happy with the decision. When I'm near the end of a long ride I'm tired enough that I don't want to worry about covers or my stuff getting wet. I just want everything to work with minimum hassle.