The issue is that this software is updated with a VIOLENT frequency that EXCEEDS the use-model of many of your users. Multiple times per week in some cases. These are not all critical security issues.
The software updates approximately one time per friggin' month. Unless there are some urgent quick fixes for showstopper bugs that users like you complain about (and rightfully so). The update popup appears one time when you start FileZilla, you can simply close it and defer the update; nobody actually forces you to immediately apply every update that arrives. After the popup is closed, the message resides in the menu bar.
At what point does FTP software become mature when I'm only using the client and connecting to servers I know??
For a software operating in a networked environment, that's easy to answer: NEVER, ever. It absolutely needs to be constantly updated, the more often the better. The bad guys aren't sleeping, either.
So, you've deliberately designed something to be as annoying as Microsoft Windows and determined that you know better than all your users how it should be handled.
I didn't design anything, I'm not a developer at all. But, the truth is, many users are incredibly lazy and ignorant of the update matter. They need to be strongly encouraged or even being forcefully fed the updates, because, if given the choice, they will never move by themselves.
Even Microsoft has correctly recognized and solved that problem, updates are fully automatic, now. There are only two things they do not consider or ignore: first are the power users who can care for their systems themselves, the second issue is that their updates are often, well, flawed.
FileZilla could also have fully automatic updates, but it asks you for confirmation. Power users can set update check to Never, but they should be perfectly capable of applying one update every three months. Being a power user is not an excuse for being lazy. And should an update be flawed (which happens very rarely, as new versions are actually tested, unlike with MS), we have a download server where you can get older installers until the problem is fixed.
Last but not least, should you really not want to update, ever, just close the popup, it won't return in the middle of the session.
I'm aghast at your design choices and the way you all are handling this feedback.
That's because the truth often hurts.