There would appear to be reason for further investigation of possibly questionable practices involving the transfer of tax-deductible, donated revenue (income) to the pockets of these pastors (salaries and benefits).
As an officer of a tax-exempt religious organization, I know first-hand that these rules are very strict. In our religious group, we carefully follow the U.S. tax code, which holds that we may not use tax-exempt donations we have received to benefit one of our employees or members - EVER!
Not even to assist a member who has become suddenly unemployed and is ill. To help one of our own members, we would have to do a completely separate, non-tax-exempt fund raising campaign. This is in accord with the law, and it seems fair to us.
I know other clergymen, who as employees of the Church, have to fill out form out 1040 and State taxes every year. Because their salaries are generally pretty meager, and they may be taxed at a lower rate because their salaries are derived from non-profits, they probably pay little tax. However, if a clergyman holds an interest in a for-profit enterprise, he would surely be paying taxes at the full rate.
As to the NPR story, it sounds as if there need to be some loopholes closed here.