Cartoons do tend to feature absolute concepts of bad guys- largely because most of them are wrapped up in a half hour and are never seen again- there isn't time for backstory and the like, as it cuts away from the action. Usually, though, IIRC (being 10 or so years removed from my last kiddie cartoon) the good guy learns a moral lesson or overcomes an imperfection of some sort. They are rarely perfect.
Now, on to Thomas the Tank Engine- man, I loved that as a kid. I'd spend hours building the wooden tracks and watching the TV shows. I vaguely remember some old picture books, but I wasn't introduced to the complete works of the Rev. W. Audrey until later in life. As such, my favorite character was always Henry. He was a lot less of an @$$ on TV, though he did have his good points in the books, as well. Donald and Douglas were some of my other favorites. I remember the old TV shows with Ringo Starr, though sadly, I was too young to realize who he was then. Ahh, good memories.