The government is an easy target here - pandering to the faith community, misusing public funds, potentially violating the Constitution in the process.

But what of the faith-based groups on the receiving end? Is this what it's come to for religion? Are religious institutions willing to become simply another Washington lobby? Compromise their voice? Earmarks don't get their own individual vote (if only). Your religious group's funds are attached to legislation funding any number of things, as  James Winkler points out below, quoted in the Times piece.

"Earmarks are bad public policy," said Maureen Shea, director of the Episcopal Office of Government Relations in Washington. "If earmarks are not in the public interest, I would wonder why the faith community would be involved in them. It would hurt our credibility."

James E. Winkler, who has represented the United Methodist General Board of Church and Society since 2000, says he fears that the pursuit of earmarks could muffle religion's moral voice. "For example, we've opposed the war since day one," he said. "But what if an earmark benefiting us -- money for a Methodist seminary, perhaps -- is attached to the supplemental appropriation for the war? You can see how very serious moral conflicts could arise."

The Rev. Richard Cizik, vice president for governmental affairs at the National Association of Evangelicals, said that while religious organizations should be able to compete for federal money, such groups "shouldn't do that through earmarks." He explained, "As good stewards of the public trust, we have to be transparent and above board -- and earmarks are not transparent or above board."
...
Clyde Wilcox, a Georgetown University professor who has written extensively on religion and politics, said religious groups would naturally justify earmarks. But their moral authority in Washington -- "the extra prophetic power of the religious voice," as he put it -- largely arises from the fact that they are not seen as self-interested, he said. "The loss of that prophetic voice would be profound."

Kenneth Wald, a professor at the University of Florida who also studies religion in the political arena, foresees a more pragmatic danger for religious organizations that lobby for earmarks. "If they start to act like any other special interest, they'll start to be treated like any other special interest," he said. "I think it's nuts to take that risk."

The best course of action for government is to refrain from entangling with religion with public money. The best course of action for religion is to refrain from seeking or accepting public money. The separation of church and state is good for both.