I think Enoch does have a point. Do we really want them to pay taxes and then claim a stake of government funding if they ever need money?
They do already.
The US has its "faith-based initiatives". Here, religiously-affiliated charities can get government grants to provide community services.
Personally, as long as they meet normal government requirements (e.g. providing services on an equitable basis to the whole community, non-discrimination in hiring, and a prohibition on using charity as a promotional or evangelizational tool), I think that religious charities should be eligible just like secular charities for government grants and other funding.
At first I thought, "well why not" but when you bring true economics into it, and you see that tax payers all get a say in where their taxes go, I feel less confident that I'd want the Church of any denomination to have a say in the matter.
I think it needs to be managed properly, but I think church-affiliated charities can have a role. Most fundamentally, they (like secular charities) have people and organizations in place that are capable of providing beneificial services to communities. Taking advantage of this fact (or at least not excluding them all as a group) allows us to reach more people and to do it more cost-effectively... when programs are managed and overseen properly.
Also, whatever else you want to say about them, churches do form the focus of many different communities within a city. Just as, say, Chinese Family Services (to use the example of one charity near me) is uniquely equipped to serve one specific segment of the population and much likely more effectively than some jack-of-all-trades organization, Catholic Community Services or the Jewish Family and Child Service also have their own niches where working through them would result in more effective delivery of services to the segments of society they focus on than could be acheived without them.
Now... I certainly don't think that any of these groups should turn anybody away who comes to them in need. If a Muslim or an atheist were to go to the Jewish Family and Child Service seeking government-funded services, I think he or she should be served just like any of their other clients. However, I also recognize that these sorts of organizations are often the best way to provide services within specific communities, and can be an effective part of an overall strategy to provide those services to the entire population.