Flatpak is good for applications where you want the people who write the software to be creating the releases and for closed source apps that you want to isolate a bit from your system.
For example, on a new system you might install everything using apt except for Zoom. Zoom isn't in the Debian repos, it's closed source and proprietary. But you can get the official Zoom application using flathub. Zoom will also be fairly isolated from the rest of your system so it has less access to your files and can be removed more cleanly later on if needed.
apt is good for most things.
Flatpak is good for applications where you want the people who write the software to be creating the releases and for closed source apps that you want to isolate a bit from your system.
For example, on a new system you might install everything using apt except for Zoom. Zoom isn't in the Debian repos, it's closed source and proprietary. But you can get the official Zoom application using flathub. Zoom will also be fairly isolated from the rest of your system so it has less access to your files and can be removed more cleanly later on if needed.