Yes, this is a fastpass attraction...
And yes, the rafts do have the covered center, however on our last adventure, my backpack got pretty wet. I think, maybe, there was water in it from a previous trip and I didn't check, because the plastic was closed all the way through our trip. So just check before you throw anything in there.
Also, on our most recent trip, there were signs posted everywhere that you most wear your shoes during the ride, so wear sandals/tevas that day!
Have fun!