I didn’t get the meaning of the question “why did anyone think otherwise”?

Question

In brief, global secularisation is not inevitable and, when it does happen, it is not caused by science. Further, when the attempt is made to use science to advance secularism, the results can damage science. The thesis that ‘science causes secularisation’ simply fails the empirical test, and enlisting science as an instrument of secularisation turns out to be poor strategy. The science and secularism pairing is so awkward that it raises the question: why did anyone think otherwise?

(Source: https://aeon.co/ideas/why-religion-is-not-going-away-and-science-will-not-destroy-it)

What does "why did anyone think otherwise?" mean here?

Answer 1

Not everything published in English represents good English. The quotation you gave is an example of badly crafted prose. What it is trying to say in its inept way is:

The purported causal link between science and secularization is so contrary to fact that it raises the question of why anyone even imagines that link to exist.

Of course, once you phrase it clearly, people may find the proposition doubtful. So there is a rhetorical advantage in expressing the thought obscurely. Not all bad prose is bad by accident.