I imagine a lot of these decisions were pretty rushed this year. There are a ton of Universities, businesses, etc, that hadn't previously done any large scale video conferencing. They didn't have much time to do a thoughtful selection.
Zoom is under scrutiny largely because it's a suddenly a highly popular choice. All the hoopla incented skeptics to take a closer look.
The fact is that almost none of the communications we use on a daily basis are end-to-end encrypted. What response would you get if you told staff, partners, executives, support personnel, etc that the new standard was based on GPG web-of-trust or hierarchical S/MIME emails and that all plain text emails (or any not digitally signed) were going to be binned at the mail servers?
For that, I don't blame organizations for doing what they had to do - it's perfectly reasonable. But the discussion that results from this is mostly healthy. Zoom will suffer from the PR but I think that will give us better options as a result going forward.