many cold air intakes, including the new K&N's also come with a protective water baffle, usually made out of foam to keep water from passing a certain point of the intake. that, coupled with a splash guard, even if you have to make something yourself, should be plenty of protection from most rainy conditions, but its still generally advised against driving too much in heavy rain...no level of protection is perfect.
one interesting project I saw on intakes was a cold air ram, which featured two longer rams that replaced the fog lamps, and used both a steep incline, and 2 water baffles on both rams to help keep water from coming in. if I can find that pic again i'll post it...was kinda slick.
and a final, and notably the BEST option...is to buy a convertible ram intake. these usually operate primarilly as a cold air ram, but the end section is removable for wet driving conditions.
naturally these are also the more expensive option, but well worth it imo.