To run a flatpak app from dmenu, you can create a symlink for the app in /usr/bin.
You can find the flatpak apps binary link in /var/lib/flatpak/exports/bin/ on ubuntu.
E.g. to run Rocket Chat (installed from flatpak via software center), you can do something like this:
sudo ln -s /var/lib/flatpak/exports/bin/chat.rocket.RocketChat /usr/bin/rocket-chat
This way you will be able to find it in the dmenu.
Resources: