No one has said that the constitution doesn't basically call for a separation of church and state, we just do not believe that asking for religious organizations to file paperwork is a violation of that separation. After all, religious buildings have to file paperwork for things like building codes etc. No one argues that synagogues and temples should be built to safety codes or that someone would inspect a church to make certain that it might safety requirements. You haven't explained why paying taxes or just filing the form to be a nonprofit is different then filing forms for a church to be built.
The reason that we pay taxes is because pooing our money together is a better way to provide roads, bridges,a police force, an army, an education etc then for each individual to do so on their own. Churches and other religious buildings are part of the community and benefit from the presence of roads and a police force. It makes sense that religious organizations would help pay for things that they use. That has nothing to do with separation of church and state.
The reason that we pay taxes is because pooing our money together is a better way to provide roads, bridges,a police force, an army, an education etc then for each individual to do so on their own. Churches and other religious buildings are part of the community and benefit from the presence of roads and a police force. It makes sense that religious organizations would help pay for things that they use. That has nothing to do with separation of church and state.