I find a lot of children's shows to be disturbing - but that's because they are simplistic. Let's look at one of my favorite culprits, Barney (I suppose I'm dating myself, here...). Most people complained that he was too goody-goody sweet. That didn't bother me - I figured my kids would learn soon enough that not everyone is nice. But what bothered me was the same thing that bothers you about Thomas the Tank Engine: an air of fascism. Yep, that's right! Ever notice how no one ever really disagrees with Barney? If anyone on the show ever wants to do something else that what the majority is doing, s/he is soon talked around. The bland conformity is almost Stepfordian - must be why my kids tired of it so incredibly quickly.