[ The Simpsons was really one of the more conservative shows on TV. They prayed, went to Church etc. The evangelical Christian character was very moral. ]
They mocked the true believers, ( Flanders ), even though he was a “good guy” they made him look like an unpalatable weirdo.
There were Evangelical groups that sprung up named after him. He was weird in the sense of his unswerving faith, charity and kindness. The point of Flanders was to have a neighbor that Homer would have no reason to dislike but dislikes anyway.