keyboard shortcut in google docs is same as safari
Unfortunately, ⌘Cmd, is almost universally the default keyboard shortcut in Mac apps for Preferences. 

As I could not find any simple way of reassigning or customizing keyboard shortcuts for Google Docs, the best workaround is to override the system shortcut for Preferences instead, to avoid the conflict.    Thankfully this can be done easily in OS X:


Open System Preferences, and then the Keyboard pane
Select the Shortcuts tab. Click "App Shortcuts" on the left pane. Then, click the little "+" below the right pane to enter our own custom
shortcut. 
From the Application dropdown, choose Safari. (Or you can
leave it as All Applications if you prefer to do a system-wide
change). 
For Menu Title, type Preferences... exactly, including the 3 dots.
Choose a different keyboard shortcut, preferably something not used by Google Docs. Perhaps ⌘CmdAlt,?


Once you've added the new shortcut for Preferences, you can use ⌘Cmd, for formatting subscripts in Google Docs!