As far as I know, one of the big differences of opinion in the movement to unify was over whether there would be a Kleindeutsch (little German) or Großdeutsche (greater German) solution. The latter would include Austria, and, given that Austria was the largest of the German speaking states, a larger Germany would be dominated by Austria, which was predominantly Roman Catholic, rather than Prussia, which was predominantly Protestant. So, number one, the Kleindeutsch approach that Bismarck took was in part a response to the cleavage between Protestant and Roman Catholic Germans.

Beyond that, once Unification happened, Bismarck still mistrusted the Roman Catholic church in Germany. The Kulturkampf (Cultural struggle) was a major factor in the first decades of Unification which saw Bismarck's government introduce a large number of restrictions to try to limit the church's influence. The Kulturkampf was complicated and I cannot do justice to a full account of it, so you could always start with wikipedia: http://en.wikipedia.org/wiki/Kulturkampf