Creating a desktop shortcut to a file in the iCloud
Apple's vision for iCloud seems to include isolating users from the confusion of the file system. iCloud files are accessed from within the application that created them–which is advantageous in some situations and a problem in others. 

To use iCloud to share documents between iOS and MacOS you'll need to install iA Writer on both platforms. (Byword fans can now do the same).

If you want to use a different text editor, or editors, on your Mac, implement my (previous?–my test of the  Byword iCloud setup is working well so far) workflow that included a storage system using DropBox.

I can't recommend this path because I haven't fully explored it, and it isn't officially supported by Apple, but if you're determined to create file aliases on the desktop, you might find a solution by exploring the folder ~/Library/Mobile Documents

↬Kirk McElhearn: Make your own personal dropbox with iCloud

Note that on the Mac I'm writing this from, the folder for my Byword documents did not exist within the Mobile Documents folder until I used the Open from iCloud… menu item. (I didn't have to load a file, just access the menu and allow the file requestor box a minute to populate.) Once the Byword folder existed, I was able to create an alias on the desktop that opens the file. I can also use the alias to Open with… TextMate but have not tested editing/saving the file using an alternative application Proceed with caution.