Actually I think the covered line queues are as much to provide cover from the hot FL sun as anything. But they serve double duty for the rain.
When it rains you just have to forge ahead with your ponchos. The one ride I will say is NOT good in the rain is Astro Orbiter. We rode that once in a downpour and had a LAP FULL of rain in our ponchos by the time that thing finished. It was miserable. Likewise I would say the Grand Prix cars are not good as they're so slow. Laugh Floor, Small World, Philharmagic, People Mover, Space, Pirates & Haunted Mansion are paricularly good with extensive indoor time. Although there's a fair amount of cover for the BTMRR queue the ride itself is mostly outdoors and I don't enjoy it in the rain. And as someone else mentioned Splash is good in the rain if you're already wet... If it's thunderstorms a lot of rides will just be shut down completely. MK isn't so good in that case as you have to wait out the lightening & thunder. Downpours are also a good time to take an indoor break for lunch.
I recommend getting some sort of weather app on your phone where you can check the current radar. We always head to something with a long wait when it looks like a particularly heavy downpour is coming. May as well spend the time wisely and have some dry time....something like Peter Pan would work in that case.