Snaps are disliked because the store is closed-source and run by Canonical. Snaps are also disliked simply because Canonical is pushing them so hard, forcibly replacing native packages that exist and work fine. For example, there was a debacle a while back where running apt install firefox still installed the Snap version instead of the native version.

Flatpaks are disliked because they sometimes struggle to integrate into a system well. For example, Discord Rich Presence doesn’t work for the Flatpak version of Discord unless the thing you want Discord to detect is also a Flatpak, and even that detection is shaky.

Snaps and Flatpaks are both disliked because they contain frameworks and runtimes that some users consider bloat.

To further explain, when you use a native package, it and its dependencies get installed on your system. If any other package in the future requires one of those dependencies, awesome, it’s already there. But for Flatpaks and Snaps, each app has to bundle its own dependencies. Sometimes they can be shared with other Flatpaks/Snaps, depending on the dependency, but they still require at least a little extra storage space.

There are probably details I’m forgetting, but those are the main arguments. My advice is if you’re happy with the way your system is running, don’t worry about it. My personal preference is Flatpak first, native second, Snap never. I don’t have anything against native packages, but some software I use is exclusively distributed as Flatpak, so I switched most things over for consolidation.