I've been through very heavy rain and never had any problems with it.
I heard this analogy a long time ago. Think of your CAI
as a straw. If its barely touching the drink barely anything is going to come up. Only when the straw is completely submerged will it flood the straw.
If you're still worried get on of these:
^ K&N Drycharger. It just fits over your Air Filter
, works great