You are ALWAYS going to pick up whatever ambient sound is in your location - appliances, neighbors, birds, surf, traffic, crickets... rain - indoors or out. Except for real sound stages there will always be ambient noise that needs to be dealt with. The trick is to minimize the affect of all this noise upon the production sound. First, of course, is properly aiming the mic (I told you that you should start aiming the mic right away...).
The second is protecting the mic from the affects of the rain on the mic itself. If you are shooting outdoors I hope you have a blimp and dead cat. The dead cat deadens the impact of raindrops on the mic/blimp. I would also suggest that you get a box of unlubricated condoms; put one on the mic before you insert it in the clip. This protects the mic from excessive moisture.
Now, when it comes to indoors, the same applies - properly aiming the mic. You should prep the room as usual, and, if they are not in the shot(s), put extra sound insulation over the windows and doors to mute the sound of the rain as much as you can.
Run several test recordings and audition them on-set. The script may have to be modified to account for the rainfall as it is close to impossible to scrub it from the dialog tracks in audio post. Also capture LOTS of extra room-tone; light rain, medium rain, heavy rain, wind-driven rain. It's a real PITA during the shoot, but your audio post team will adore you for it.