This is a huge weakness in the IRS system. It inhibits free association while infringing on first amendment rights. Why should any of these groups had to register in the first place? So that government can collect their money? To need this sort of governmental permission of form and organize goes against the grain of the first Amendment.
A flat tax doesn't even fix this matter. We need to shift to a consumption tax, and get the federal government out of the business of approving what and how Americans can organize.