If you have a bottle of water with a twist cap, they won't harass you about it, in my experience. No eating at all though. Florida has too many bugs that would love to find a feast on the bus, and most people don't want to share a bus with them. Also, if someone makes a mess and the bus driver has to clean it up, it would slow down the whole system.
And that applies to both Magical Expres buses and Disney resort buses.