This brings up an interesting point, should religions be taxed?
IMO, we should just take "advancement of religion" (or similar wording, depending on the specific country) out of the list of charitable causes and let religious organizations end up with whatever status they warrant.
Considering the characteristics of a typical church (doesn't make a profit, most of its activities are primarily for the benefit of its own members) and going by Canadian rules, I'd say most churches would probably qualify as not-for-profit (so would pay no tax), but not as a charity (so donations to them wouldn't be tax deductible). I think that's a fair treatment for churches that's in like with other types of social clubs.
In the US - from what I understand - there isn't this sort of difference between a not-for-profit and a charity, so a church might still keep its tax status even if we ignore its religious nature... fair enough.
The main thing for me is just getting rid of special treatment for churches: no clergy housing allowance, no exemptions from normal rules, no exemptions from filing requirements, etc.