Oh boy, where to even start?
Well, with Flatpak, because it’s a much lesser evil of the two. In fact, it’s not really that bad. The only issue I have with the concept of flatpaks is that they statically link all or most of their dependencies and do not integrate well with the system. The obvious downside of statically linking dependencies is that flatpaks use a lot of disk space. A less obvious, but perhaps more serious disadvantage is that older versions of dependencies may lack security fixes. But in spite of that, the concept is not necessarily bad in every situation, because sometimes you want to be able to have separate versions of dependencies. However, I find the AppImage format to be far superior for that.
Snaps, however, are an entirely different issue, due to snapd, which is spyware. When I say that snaps are spyware, I don’t mean individual applications, even though malware has been found again and again in snap packages, but I mean snapd itself. It has telemetry that cannot be disabled, and it collects identifiable information about you not only every time you install a snap package, but also every time you use it (it collects usage statistics, per user, per package). While snapd running on your machine is open source, the server side of it is proprietary. All of this data is collected by Canonical and you only have their word that they are not going to abuse it (for example sell it to a third party to serve you ads, or even worse). Canonical’s word regarding privacy is of little worth, given their history.
There is little advantage to using snaps over flatpaks, but there is this huge privacy issue, so if you are using snaps, my advice is to stop and find an alternative. Most of the software that is available as snaps and flatpaks is also in the AUR, which is a completely transparent system and, if you are careful and know what you’re doing, perfectly safe.
I hope this has shed some light on why people are often negative about flatpaks, and especially snaps. There are legitimate concerns, it is certainly not all bashing and irrational hate.