So I wrote to disney again asking about the rain issue. I said I was told it runs rain or shine but yet I am hearing stories from people of the service stopping or being dropped off outside the gates. Here was the response.....
Thank you for contacting the Walt Disney World® Resort.
The Express Transportation Option travels directly between each of the theme parks—with no other stops along the way. Weather would not change the course of the buses, unless they are inform of any safety hazards, they would drop you off inside the main gate, so you're in the middle of the park from the moment you arrive. If there are any changes, they would notify all guests in advance.
If you have questions or need further assistance, feel free to contact us.
So the possible safety hazard is mentioned but not saying it what that could be.