“It’s not just the housing that they don’t pay taxes on, but often the lower rate that they in turn end up paying on that part of their tax that isn’t exempt.”
That is no different than just like the “lower rate” any taxpayer with deductions gets to after the deductions are taken.
Actually, with the average salaries so low and depending on their actual housing costs, many ministers are no different than the average taxpayer - taking the standard deduction, which is generous, instead of itemizing deductions.
Salaries are so low because they get their housing “free”. And if they are given housing they are less likely to have a mortgage, which is the reason most people itemize.
Yes, others with deductions get a “lower rate”, but this is a massive deduction and the impact is indeed for them to pay lower taxes on the rest of their income as well as no taxes on their housing income.