"Because"
(I) It is ironic, not tragic, that minorities in our country have come to be identified with religion and not with community or profession.
(II) The establishment of many such organizations are testimony to the growing antagonism to secularism.
(III) Secularism today is being taken as a threat to religious identities, to the existence of religious diversities, though secularism was never conceived as such.
(IV) This is the reason that secularism today has come to mean as preservation of religious minorities in their traditional modes.

"Because" introduces a reason or cause for the first statement. The second statement should explain why the first statement is true.

We look at the meaning of each of the four statements provided.

I: Minorities are identified with religion (not community/profession).
II: Organisations show antagonism to secularism.
III: Secularism is wrongly seen as a threat to religious identities.
IV: Secularism now means preserving minorities in traditional modes.

The combination that makes the most sense here is Option B ( I-IV): "It is ironic, not tragic, that minorities in our country have come to be identified with religion and not with community or profession, because this is the reason that secularism today has come to mean as preservation of religious minorities in their traditional modes." This presents a cause-and-effect dynamic and explains why minority-religion identification is ironic (due to secularism's distorted meaning).

The other options seem a bit forced. Option A( II-III) and option D(I-II) show no clear cause-and-effect relation. Option C(III-IV) is also not correct because both statements are parallel observations. 

Therefore, Option B is the correct choice.