@Muhd I don't see how you can assert that it's Protestantism. That's as absurd as asserting that it's a deliberate secularization. Anglicans have saints.

@Mr.ShinyandNew安宇 Anglicans are a rare exception to Protestants generally, who make a point of referring to apostles by only their names. If you look at the discussion in this thread, it's pretty clear that the nations where saint thomas is used in the expression are historically Catholic nations, and the ones where it is merely "Thomas" are historically protestant nations.

Further, anyone familiar with the biblical Thomas would never think "doubting Thomas" referred to anyone other than the apostle Thomas. At least, I wouldn't.

@Muhd I don't think that's sufficient to prove that the "saint" part was deliberately left off as a snub of Roman Catholicism. Also, it's relevant that Anglicans are exceptional when it comes to Protestantism, since Anglicans speak English. In any case, in Quebec French, as Alexandre noted, the "saint" is left off, and they're totally Catholic.

The use of Thomas as an allusion to the Apostle pre-dates Anglicanism. Sadly the OED provides scant examples so we can't know for sure if, before Anglicanism, people always said "Saint Thomas".