Churches/Charities/Not For Profits should all pay tax on all income (including donations) and then get a tax concession on any money actually used for charity purposes (that help arms length individuals avoid complete poverty and starvation). That would put these leaches on same footing as every other individual and every other company within our society by remove their tax free property development businesses, tax free retail businesses, etc..
In fact the whole tax system needs an overhaul so that double Dutch/Irish tax bullshite and other rampant tax cheating methods used by multinationals (which Churches/Charities/Not For Profits are just another part of these cabals) can be eliminated. That way they pay their fair share and thus support the infrastructure which they use while also supporting the other needs of the society in which they operate.
I tend to agree - get rid of most of the tax rebates and concessions and simplify the tax system. If a business or enterprise needs some sort of public contribution to be viable then they can make their case to the government and the government can pay them openly and accountably for their services.
The rebates and concessions tend to make the tax system a game, rather than a civic duty to support public infrastructure and services.
I reckon that there should be taxation a KPI that requires a tax return to be manageable be most all tax payers. The idea that a typical tax payer needs to use an accountant would be a symptom that the tax system is either too complex, or people, are paying to game the tax system (or tax accountants are pulling the wool over some tax payers eyes).