Except that they get tax breaks as charities.
Actually fundamentally I have no issue with all charities having the same tax breaks but there are a range of issues here.
First religious organisations are simply allowed to be charities simply because they are just that, religious organisations. They don't have to demonstrate any further benefit to society that other organisations need to do to be given charitable status.
Second, and linked to the above - religious organisations get tax breaks for everything they do, while many other charities will only get breaks on those activities deemed to be charitable, while other activities don't have that status.
Third - many churches get the status automatically without having to apply, register, provide paperwork to the charities commission (under the excepted charities rule). Non religious charities with turnover of over £5k must go through the registration process etc - if you are a church you are exempt from that paperwork unless your turnover is over £100k.
Finally the business rates issue I raised earlier - if you are a (non religious) charity you still are expected to pay 20% of the business rates on your premises, rising to 100% on commercial activities (e.g. cafe, shop etc). Churches are completely exempt from business rates and in most cases this includes space used for cafe, shop etc. The buildings aren't even on the list of eatable properties.
So I've no fundamental issue with religious organisations benefiting from charitable status, but there should be a level playing field with other charitable organisation.