Flatpak is fine. Snap is Canonical's proprietary version, which ties you specifically to their app store. It's not designed to be an open standard but Canonical has made it compulsory in one of the largest distros (Ubuntu) and its derivatives. There are also problems with its sandboxing mechanism competing with AppArmor.
AppArmor and SELinux sandboxing stuff pushed me to only install services with Docker on my headless machines 😣 found out most services can't write to their own homefolder
There was an Ubuntu developer that left Canonical about a year or so ago. His reason was that he had spent a number of years (possibly over a decade, can't remember) optimizing some code and the kernel to get the fastest boot time possible.
Then he saw Canonical practically throw his work out the window by introducing snaps, which until recently was plagued by serious slowness on the first start of a snap.
He said it felt like his years of work just meant nothing at that point.
There are a number of reasons Flatpaks are a better open source option, even if they aren't perfect.
This hate comes mostly from Linux communities like here and on Reddit. When you see actual numbers, both are widely used for production use. They have lots of active users as reported in their respective blogs and websites.
That said, it is aware that both had problems. Most hate towards Flatpaks that I can see is from purists that prefer their distro shipping their packages with dynamic dependencies and uprated by their package manager. Also there is complains with outdated runtimes and stuff like how sandboxing works.
Snaps has all problems than before with some extras. When they were released, because of compression, they were painfully slowly to open and they affected boot time. Nowadays this is mostly gone, but they still keep a proprietary store, inability to have multiple repositories (stores) and they don't respect your home directory structure by placing a "snap" folder in your home.
Personally I use both and I'm happy with them. The proprietary store stuff does not bother me because I'm already trusting canonical binaries by using Ubuntu and they are easy to use and be productive with them.