The monorails are perfectly safe in a thunderstorm. Might be scary, but it's safe. I actually was on one in July of 1994 when it was hit by lightning. We were stuck for a good hour or so on the track, but everybody was fine. When I went in 2006, me and my GF had just arrived for our first night and since we didn't want to waste a day of our pass we decided to take a trip around the Seven Seas Lagoon (she had never been before so she was excited)! There was a huge thunderstorm occurring and it was breathtaking to say the least! We ended up doing two full circles around the lagoon before we got back off at our hotel. I never have ever felt unsafe during a storm on the monorails. Honestly, it should be as safe as being inside a car during a storm.