I've loved Thomas since I was a kid and I don't know why the movie gets a bad reputation. The music and Peter Fonda's acting are worthy of an Academy Award. But there are some flaws. First of all how does Thomas get to the coal car? There's only one track! And second where is everyone? The island looks like the rapture happened everyone's disappeared. Many of the characters: Edward, Duck, Mavis, Donold, Douglas, the narrow gauge engines etc. are absent!
So as I said, good but flawed. I still don't understand why so many people hated this movie. It is and will always be a childhood favorite that I will pass on to my children.