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Interesting article.
Its really about worldviews which I define as the core presuppositions (fundamental assumptions) on which entire belief systems are based. Misunderstandings and disagreements often stem from having different worldviews and hence disagreeing on the logical conclusion.
One persons beliefs may seem illogical to another person if they are being viewed from a different worldview, even though those beliefs may be perfectly logical deductions from that person's worldviews.
Its interesting that the author separates those who "have faith" from those who "refuse to believe anything that is not backed by logic", clearly showing her own bias! She even calls it "inexplicable" - from her worldview such faith cannot be logically deduced. She is either failing to understand these people's worldviews first to see how they came to their conclusion (analysing the conclusion from her own worldview), or she understands their worldview and can see a flaw in the logic (I suspect it's the former).
So how do you tell which worldview is correct? Not easy, although we can be sure that if a worldview logically leads to a conclusion that is inconsistent with reality or itself (a contradiction), then it is as a whole flawed.
Of course a contradiction with reality is basically a contradiction with the popular presuppositions about what we observe being real.
For example if you assume that the earth is flat (after all it looks like it is from its surface), then you fly into space and see it from space, you have 3 choices:
In conclusion I don't think you can ever understand another person's beliefs unless you can put down your own worldview and try to understand theirs, otherwise you'll simply be trying to understand them in the wrong context and the chances are it will seem illogical to you.