You can't:
- Easily backup to a previous version if you don't like the latest changes made by the company/developer
- Run two of the same versions on the same machine (some programs will even let you run different versions simultaneously)
- Backup programs and settings easily (there is no standard for where settings are saved) and if the original site goes offline without mirrors, you may not be able to use that program anymore.
- Run a program entirely inside an encrypted volume (like VeraCrypt or TrueCrypt)
- Easier to make available on multiple computers (installed programs require that you go to each machine and go through an install process or re-image computers with the latest install)
- Let you easily run a program or tool on the fastest possible computer available to you, important for 3D, CAD, and video editing/conversion.
- (Everyone here knows this but I have to include anyway) Run a program over a cloud drive or from a USB stick