No it isn't. It is about how much an individual can verify where the money that they are taking in is going.
Bingo. If I donate money to the Red Cross earmarked for distaster relief, the Red Cross is
obligated to use that money for that purpose. If I give money to Harvard University to buy scholarships for minority students, they need to spend it on minority students. If they don't, they are criminally liable (for fraud) and civilly liable to me. There are a number of cases out there where people have successfully sued to have donations returned because the organization has misused their funds.
Faith-bsed organizations are, for the most part, the only types of non-profits for whom the public has no such assurance. If I give money to Harvard, I know where the money goes -- they have to tell me. If I give money to Boston College (a "faith-based" college), however, they can spend the money however they like and there's not a damned thing I can do about it. "Well, drkitten
did specify that this money should be used to create a new department of Feline Studies. But we're going to use it all to re-guild the chapel. Bwahaha. What can they do, sue us?"
In simple terms, I can't even check out how "efficient" the charity is. Personally speaking, I refuse to donate to the United Way (a fact that ticks off my dean to no end every year, I assure you). Their overhead is simply too high; last time I checked, about eighty cents of every dollar donated goes to salaries and administrative overhead, so I need to donate a fiver to make sure that a single dollar gets to the charity of my choice. I'd rather simply send the fiver directly than buy new carpet for the local United Way chairman.
This information can be gleaned from forms like the 990. The local secular food bank is volunteer-run and staffed, and something like 97 cents on each dollar goes to feeding the homeless. I know this because they told me so on the 990. There's also a local Catholic homeless shelter that runs a soup kitchen, and I have no idea how much money they spend on food, because they don't tell me -- and they don't have to.
I think that "licence to commit fraud" is a pretty big difference in the way that groups are treated.