You aren't really subsidising it, unless you're making the argument that if organisations - such as Hillsong - paid taxes the overall tax rate would be lowered for all? Ideally this might be true but the cynic in me suggests it wouldn't... well, that and the fact that their income within a given country is relatively insignificant as compared to GDP within that country.
Moreover:
1) Hillsong runs substantially on donations and purchases of their merchandise (including music). Most of the people who give or buy their merchandise are taxpayers themselves.
2) Anyone paid as an employee by Hillsong will pay taxes, just like everyone else. I don't know much about the lifestyles of their senior employees/leaders - maybe it's a televangelist-style Gulfstream-and-champagne-fest, maybe not.
3) We know Hillsong earn a lot of money but we don't know that they keep very much of it[1]. If they're anything like HTB, they quite likely don't[2]: the vast majority will be spent on staffing, ministry, along with a chunk given to support other organisations and causes. Ministry means everything from what you see on a Sunday and special events through to social initiatives such as food banks, homeless shelters, childrens' work, soup kitchens, and educational initiatives (and more) that many churches either support or run.
Point (3) is important because it's the point that makes a church a net good within society (or not, in the absence of it). If they're not a net good then I'd be more inclined to agree that, yes, they should be taxed as businesses rather than not taxed as though they're charities. Quantifying that is obviously non-trivial.
[1] It's possible they do but I don't have any information to hand on this.
[2] At a pure numbers level this is something that distinguishes a charity from a (healthy) business: one does not generate a profit (which is not to say the money shouldn't be used carefully and beneficially: clearly it should), whilst the other does.