I think you are incorrect.
That's productive.
Again, when the Constitution says that Congress shall not make laws "respecting an establishment of religion" it means that Congress should not make laws that contemplate, consider or treat (i.e. "respect" in a legal sense) a specific religion as if it were an official state institution (i.e. an "establishment of religion" in the legal sense).
The faith-based inititatives do not single out any religion for treatment or consideration in a way that approaches that religion as if it had official status.
What they do is remove an existing bias against all religious institutions: the law does not even favor religion in general - secular non-profits are as entitled to funding as non-secular ones - let alone any specific religion.