depends on where you are!
if its raining, yes, SOME rides stop operating. Mainly those that have an outside section, such as Test Track. During inclement weather, Test Track ceases to operate. I've never been in line during a storm, so i don't know if people in line are given passes to come back or not.
I would imagine that other rides that go outside (off the top of my head, Big Thunder Mountain, Kali River Rapids, Dumbo) also operate on the idea that rain (and especially lightning in that part of florida) would be reason to shut down the ride during a storm.