Madison thought that the 1st Amendment does not permit government funding for religious charities -- and knew since he wrote it:
http://en.wikipedia.org/wiki/United_States_Bill_of_RightsTo the House of Representatives of the United States:
Having examined and considered the bill entitled "An act incorporating the Protestant Episcopal Church in the town of Alexandria, in the District of Columbia," I now return the bill to the House of Representatives, in which it originated, with the following objections:
. . . .
Because the bill vests and said incorporated church an also authority to provide for the support of the poor, and the education of poor children of the same; an authority which being altogether superfluous, if the provision is to be the result of pious charity, would be a precedent for giving to religious societies, as such, a legal agency in carrying into effect a public and civil duty.
http://www.constitution.org/jm/jm_estab.htmJune 3, 1811
To the Baptist Churches in Neal's Creek and on Black Creek, North Carolina.
I have received, fellow-citizens, your address, approving my objection to tile Bill containing a grant of public land to the, Baptist Church at Salem Meeting House: Mississippi Territory. Having always regarded tile practical distinction between Religion and Civil Government as essential to the purity of both and as guaranteed by the Constitution of the United States. I could not have otherwise discharged my duty on the occasion which presented itself. Among the various religious societies in our Country, none has been more vigilant or constant in maintaining that distinction than the Society of which you make a part, and it is an honorable proof of your sincerity and integrity, that you are as ready to do so in a case favoring the interest of your brethren as in other cases. It is but dust, at the same time, to the Baptist Church at Salem Meeting House, to remark that their application to the National legislature does not appear to have contemplated a grant of the land in question but on terms that might be equitable to the public as well as to themselves.
Accept my friendly respects. JAMES MADISON.
June 3d, 1811
http://www.constitution.org/jm/jm_estab.htm(Note that at the time of James Madison, the Baptists, a minority religion then, were strong supporters of the separation of church and state.)