At the point when the Plantation was being proceeded with, religions - both Catholicism and Protestantism - were in a fairly powerless position.
There had been the appointment of some Protestant bishops in Ulster before the Plantation took place, but their principal activity had been in trying to identify what lands they could lay claim to, to support their positions, rather than to engage in any evangelical endeavours.
On the Catholic side, that there had been significant destruction of property, in that sense most churches would have been destroyed during the course of the war. Their lands would have been despoiled, again during the course of the war itself, both by the Irish side or the Ulster side while they were waging war against the Crown, and then subsequently after the Crown forces came into Ulster, there would have been a massive destruction as well.
So that in that sense, both churches, if you want to look at things in Protestant and Catholic terms, both would have been in a weak position; that the Plantation of Ulster of course further weakened the Catholic church, because it had no legal standing; but, on the other hand, a significant number of people from Ulster went to the continent, were trained at seminaries, and they returned in an altogether more evangelical mind and better-educated in their faith, than would have been the case previously - in that you had now a counter-Reformation trained clergy available on the ground. And it is quite evident that they are there in significant numbers in the 1620s and in the 1630s, even though there was a relatively small amount of patronage available for them.
The Protestant church, on the other hand, benefits substantially because one of the considerations in the designers of the Plantation was to provide liberal endowment for Protestantism. Specific estates for the church are laid aside, there is an endowment for Protestant schools - one in each county - and there is an endowment for Trinity College Dublin which was to have a responsibility for training of Protestant clergy who would engage in the evangelisation of the population.