Again, not the issue. Atheists question the validity of where the money goes. You and I both know very well that some of it goes to pay pastors, secretaries, etc, and they pay tax on that income. Even if it is exorbitant amounts of money, it's still taxed on a personal level. Charitable giving? Again not in question. What IS in question to them is whether a 50 million dollar jet is in any way, shape, or form a part of evangelism and free from being taxed. Some extreme atheists think that even reupholstering the pews shouldn't be tax free. I disagree with that, but it's a valid argument.
Again, just eliminate the tax code and it all goes away. The root problem isn't who is getting the benefits of it , it's that the system is inherently flawed