The only "tone" in "I've never understood why bible fanatics are so fixated on that story, it's one of the bible's most conspicuous flaws." is the one you've projected onto it. On its face, it's an honest statement of lack of understanding. It was neither unnecessarily offensive nor was it unnecessarily derogatory. You only see "tone" because it doesn't support or affirm your worldview.

Additionally, even explicitly saying, "Anyone who believes the bible is the literal word of God is an unwise and foolish person" isn't intolerant. Intolerance is more than just disagreement. Intolerance is saying, "You should not be allowed to think those thoughts," not just "If you think those thoughts, you're unwise and foolish." It's unwise and foolish to think that jumping off a bridge will solve your problems. It's unwise and foolish to believe that vaccines cause autism. Many things in this world are unwise and foolish, and it's meaningless to claim that whenever someone refers to a belief as unwise and foolish he's somehow "intolerant" of those who hold that belief.

It is no more "intolerant" of me to say "If you believe the Bible is the literal word of God you're being unwise and foolish," than it is for me to say, "If you believe that programming languages should be dynamically typed you're being unwise and foolish." The only difference is your sensitivity to those claims.