Granted, people such as Ray Comfort just give themselves very generous perks from their "ministry". I imagine that other religions would do the same if they wanted to, which again brings us to the fact that removing the tax exemption wouldn't be an issue as they shouldn't have to pay tax if they're actually non-profit.
As for your two examples:
If you tax parking, then you're taxing everyone, and giving the rebate to a specific sector. This already happens. Everyone has to pay sales tax (for example), and the state tends to throw money at organisations they like anyway.
As for halal butchers, surely they're already taxed because they're businesses (at least they are in the UK). Similarly, I imagine Christian bookshops have to pay tax.
The irony is that out of all the religions you could have chose, Islam is the worst. They're [generally] pretty particular about money - for example not being allowed to charge interest, etc. Out of all the religions I'd been concerned about not paying tax, Islam isn't one.
Doing a quick google about Islam and paying tax I came across this nugget - it's not exactly related, but it show's how dodgy some people are and how they'll try using their religion for any reason:
Is it permissible for him to cheat a kaafir government and take money from them? - I'm glad he was put in his place by the people answering.