As long as you have the skidplate under the car and the inner tire fender well yuo'll be fine as long as you don't drive into a DEEP puddle that you shouldn't drive in anyways. I've had my CAI for years in multiple states and when it rain here in AZ IT RAINS! You shouldn't have a problem with a true CAi, but if you're really concerned go with the SRI. Even a warm air intake is better then the factory crap.
Current 2012 stock Focus
SOLD 2006 ZX3 SAP, Draxas Header, MBRP exhaust, CAI, Tuned, Debaged, FRPP lowering kit, SVT 5spoke wheels, Black Halo Projector Headlights, Niteshaded Side markers/tails, Mazda rear wiper, mustang antenna