Many organizations such as Yeshivos classify themselves as “synagogues” specifically for the purpose of getting out of filing public 990s. If donor would show their disapproval and insist on transparency that would shift the tide.
You may be very surprised to see the salaries of the staff of some non-profits. Several heimishe mosdos have execs making $400k or more in DECLARED income. This does not include other non-declared income and benefits such as parsonage, trips to Israel etc.
It is a shame that so many people give tzedakah with just their heart and not the mind as well.