Exactly. The problem is that whistleblower protections come from the government. The courts cannot be trusted to always have your back. Hell, I would go further and outright assume that they will blatantly favor corporate interests.
I do not blame someone for not wanting to risk the exposure.
In this case I'd stress that the FAA itself cannot be assumed to "have your back", given their coziness with Boeing
(although I can't know if the whistleblowers were truthful)
To be clear: mainstream major media publications use anonymous sources all the time. The point here is that the whistleblower be talking to the Times or the Post[1] and not "View from the Wing". No one is demanding they come out in public to tell us who they are.
[1] And let's also be clear: journalists from both those organizations are surely on the phones full time right now trying to find dirt on Boeing quality processes. That would be a huge story if they could land it.