To prevent the automatic creation of a "My Articulate Projects" folder

Articulate 360 creates that folder and, as Phil said, uses it as the default location for publishing. 

You can still set up your own folders for each project, and browse to the appropriate folder when publishing. Those folders could be inside the My Articulate Projects folder—or not. (My preference is "not.") 

If you don't publish to it, just leave the My Articulate Projects folder empty. Or use it to store miscellaneous files related to Articulate 360, such as demos from tutorials that might be useful for reference.