In what sense is this "lost money"? Are you proposing to start taxing other charitable and non-profit organisations?
Calling religious institutions "charitable" is not entirely honest. Yes, many of them do donate large sums of money to charitable works, and I have no problem with those specific funds being tax-exempt (if I donate to a charity, it's tax-exempt as well).
But many so-called "religious institutions" are most definitely run for profit. Televangelists are a perfect example. There's no reason whatsoever to consider the entire organization tax-exempt simply because some of them occasionally do some charity work. Let them write off their charitable contributions just like the rest of us do, and tax the rest of the organization normally.
There's no reason at all that an organization should be considered tax-exempt simply because they believe in some magic hoopity.