It's not really as much of a problem as people tend to think. If the nipple is dry, the cap is dry, and your hands are dry when you cap the gun, and the cap is a good fit on the nipple, you've pretty much got a waterproof system. If it's raining there's more chance that water getting in the bore will ruin the charge than water at the cap.

I keep a small chunk of beeswax with my gear. If I'm going out in a real soaker, I'll warm up the wax with my hand, rub a little off, then rub it around the cap after it's on the nipple. Never had any problems.