Early Simpsons did satirize Christianity a bit but didn't go full blast with it because they already had their hands full with just satirizing the idea of a "normal", wholesome American family that ironically corresponded less and less to the way people were living their lives at the time. We now see satire of American Protestantism as a desirable thing, but it wasn't as desirable as it is now in the early 90's even though people obviously wanted to see some of it.

Flanders looks like a poor foil because we no longer see Homer's family as scandalous. He is indeed a good 'straight man' (in the comedic sense) but early Homer is no longer as goofy so we fail to see it.