Look at that, argumentum ab auctoritate, you must be right then!!
What I read was that the show was conceived has an invitation to people of every beliefs, never anything conclusive about what those people should find in it or what the show would tell them concretely. But going to Flanagan and what he said, you're right, doesn't take much "deep thought" to understand where he is going...
“I was shocked, for the first time comprehending what a really strange book it is, [The Bible]. There were so many ideas I’d never heard before in church, and the violence of the Old Testament God is terrifying! Slaughtering babies and drowning the earth! It really struck me that I didn’t know my faith at that point. [...]”
And also from The New York Times: "Like Riley, Flanagan spent years studying various religions. Ultimately, the books that most spoke to him espoused atheism, rationalism and science — books by Samuel Harris, Christopher Hitchens, Carl Sagan. “I had more of a spiritual reaction from reading ‘Pale Blue Dot’ than I ever had reading the Bible,”"
And from Vanity Fair: "Flanagan was raised Catholic and served as an altar boy at his parishes on Governors Island in New York and in Bowie, Maryland. That history heavily inspired the setting, along with other doubts and philosophies he developed as he grew up and tested those old beliefs. “This isn’t about just Catholicism, it’s about the traditions of all of our religions, especially ones that reach back into the ancient world,” Flanagan says. “The ancient world was a bloody and violent and terrifying place where we didn’t understand the nature or the weather, or whether we’d live through the night or through the season. And every single natural function of the planet could be made to feel like a supernatural attack.”"
Now I'm not saying your quote about the show aiming at teaching others empathy and acceptance for others' beliefs doesn't exist - I couldn't find it with a quick search, but it might exist - I'm just saying that's not what the show does, and that thinking otherwise is still probably a reaction to cognitive dissonance.