Note that Flutter uses GTK3 on the Linux desktop.
For the same reason that so many Electron apps exist: it’s easier for developers.
As a user, I really like GTK3/GNOME applications. They often look great, respond quickly and are really easy to understand. As a developer, however, I find it very hard to use. It has a steep learning curve and has all the issues of a niche project without strong commercial backing.
So what’s the alternative? Electron?
Flutter is a great compromise: it’s almost as easy to use as Electron, but it creates native binaries and has native integration with GTK. Given that Google pushes it so much, there is a high chance that many developers will know how to use it.
So, in the context of “we want more people developing apps for Linux”, I think this is a great decision. With such a core part of Ubuntu using Flutter, Canonical will be forced to make sure Flutter works great on Linux. This has the potential to get a lot more people contributing to Ubuntu and developing apps for Linux.