A Wisconsin-based group of atheists and agnostics has brought suit against the Bush administration's promotion of federal monetary aid for religious charities in the case Hein v. Freedom From Religion Foundation Inc. But the first issue the Supreme Court must deal with is whether the group has standing as taxpayers to bring suit. Precendent comes from Flast v. Cohen, in which taxpayers sued over a Congressional statute which funded instructional materials for parochial schools. The group was granted standing and the law found unconstitutional, but the Court limited standing to cases that show the legislation exceeds specific constitutional limitations upon the exercise of the taxing and spending power (and not simply beyond the powers of Congress in general), though it has been narrowed even further in later cases.
Obviously, the Court can't grant standing based on general grievances of a taxpayer or everyone in the country could bring suit over in expenditure they didn't like. Without making a judgment on whether faith-based initiatives are constitutional in themselves (which is another topic), clearly granting standing here would be in keeping with the principles of Flast, though admittedly it's unlikely the Court with its current make-up will choose to do so. It's interesting that the administration is fighting this so hard because you'd think conservatives would want to broaden taxpayer standing to challenge governmental programs. I guess not when they are supporting religious groups, eh?