The income of the church (ie. donations) is generally not taxed, whereas the income of other businesses is. As mentioned above, some clergy in some jurisdictions have favourable tax treatment of their salaries.
The income of "other businesses" is usually provided in exchange for a service. i.e. I sell you soap, or mow your lawn, and you give me money. Churches don't operate that way. If they do, then they are taxed. i.e. if a church operates a coffee shop, the coffee shop is taxed.
In general, if an organization subsists on donations, it isn't taxed, and the donor gets to take a tax deduction for it. There are some guidelines that have to be followed, but, as the IRS guidelines state, these aren't any different for churches than they are for other not for profit 501 C(3) organizations. So, they get "preferential" treatment compared to businesses, but not compared to other non-profits.
There are usually more classifications than commercial, residential and other (eg. industrial, institutional, etc.) In many places, churches don't pay property taxes on church buildings, or get preferential treatment.
Well, yes, a factory is classed differently than a retail store so calling both "commercial" isn't correct. However, most buildings consist of either
1. Places where residents live or
2. Places where people operate money-making ventures.
Residents pay taxes to support their city of residence, and when you make money, the government takes some of it. That's pretty well understood.
If a building is neither someplace where someone lives, or someplace used by someone to make money, it generally isn't taxed. Examples include charitable organizations, which are generally exempt from tax. I don't know how non-profit hospitals are treated. I suspect they are taxed, because they charge fees for their services, generally.
Personally, I would remove favourable tax treatment for clergy salaries (which would include disallowing such things as "housing allowances").
I would suspect that the housing allowances have an interesting legislative history, that probably started with a question of how to tax church-owned property where people, such as nuns and priests, happened to live. This raised the question about whether to tax them as residents, or leave them untaxed as part of a non-profit organization. Because the US was favorably disposed toward ministers at the time, they probably erred on the side of the church. Then, some congressman somewhere probably decided it was "unfair" to give a tax break to a minister who lived in a church owned parsonage, but not to one who paid his own rent, and so introduced a "housing allowance".
Whatever the history, it does seem inappropriate to me to give a tax exemption for a minister's "housing allowance". I would favor ending it, but again, it's not something I would get up in arms about.
I would also tax church property less favourably. In terms of the income of the church (ie. donations), I would not make the church pay income tax on its donations, and I would keep the tax-deduction for the donors, but I would put in place a requirement that the church use a certain portion of its donations for the general good, not for proselytizing or for the benefit only of members.
As Jim and Tammy Bakker found out, there are restrictions on how churches can use their money, and if they violate those rules, people can, and do, go to jail. (That's a good thing.) If you try to create a private club, and call it a church to avoid paying taxes on the clubhouse, you will be in trouble with the law. As for proselytizing, the IRS treats it as any other activity which provides no particular benefit. If I start a not for profit organization whose purpose is to play tiddlywinks, I can probably manage to get a tax exemption as long as I can convince the IRS that it isn't just the members playing tiddlywinks. (i.e. if I make tiddlywinks games open to the public on at least some occasions.)
In other words, the preferetial tax treatment of churches is greatly exaggerated. For the most part, they are treated the same way as other organizations that subsist on donations.