Questions about using Ubuntu, the operating system, are on topic. Using an OS includes using applications running on that OS. That's pretty much all that using an OS means. So if we were to make questions asking about software not developed by Canonical off topic, we would have a pretty small site.
Basically, any software that runs on Ubuntu is on topic since we want to provide support to users of Ubuntu. Canonical develops and maintains a tiny number of tools. The vast majority of applications on Ubuntu (both those installed by default and those in the Ubuntu repositories) have absolutely nothing to do with Canonical.
For instance, should we make questions about using KDE off topic? Or Gnome? If your wireless doesn't work, should we send you away because the drivers aren't made by Canonical? What if you have a shell scripting question? I can think of very few questions on the site that are actually about programs developed by Canonical. Apart from questions about Unity, pretty much everything else on the site is about software not directly developed by Canonical. After all, the Linux kernel itself isn't developed by Canonical (although they do modify it for the Ubuntu kernel, the main developers are the Linux Kernel Group) but we can't make the kernel off topic!
So, in short, questions about using software running on Ubuntu are essentially about Ubuntu, and Canonical only maintains a tiny percentage of the software present in Ubuntu so limiting this site to those only would essentially make it useless.