Had a particularly annoying time with this as the document sets were already in use and was attempting to do this in SharePoint Online. My scenario was that I was using document sets and only wanted document sets in the root folder. So I set the other ctypes as not visible, but then the customer asked to default to one of the content types that wasn't previously set up at the top of the list, and I couldn't reorder in the "Document Set Setting" option of the document set content type because there's a multi-select box with no up/down functionality for these. As a last ditch effort I went back to the List Settings and just made all content types visible on the new button, which enabled the documents that were supposed to created in the document set to be created at the root level (temporarily). Then I reordered the content types, then set the non-docset content types back to not being visible. VOILA! to my surprise that solved the problem.
I had previously tried to reorder them but I didn't make them visible first and it didn't work.
Hope this helps someone else spend less time scratching their head.