I always heard that the Acadians were expelled by the British for primarily loyalty rather than religious reasons (Seven Years War/French & Indian War). I think a lot of the ones who ended up in Louisiana were originally deported to France and then "retransported" to Louisiana by the Spanish (who then owned the place).
I do think it was a combination of both. The French Catholics did not like them, and the English saw them as a threat as well. The Spanish were happy to have more settlers in their territory. Apparently when you are unique - you are often feared -misunderstood and dis-liked.
Of course - to me...that only means "you must be onto something..keep it up"