If this doesn't discriminate by religion, I think I'm okay with this. As long as mosques, synagogues, Buddhist monasteries, Hindu temples, Wiccan covens, Scientology centers, and Ramtha's School of Enlightenment all get equal funds for their size, I don't think it should violate the 1st Amendment, and I say this as an irreligious person.
That being said, I have no faith in this administration to enact this in any kind of equal manner. It's hard to tell from the article what organizations are eligible, since the writer seems to be using "churches" and "faith-based institutions" interchangeably.