Step 1: open the terminal from the applications
Step 2: type "cd /opt" without quotes.
(I assume that you've not changed the default installation folder for google chrome. If not so, go to that directory where chrome is installed)
Step 3: type "cd google" , then
"cd chrome" without quotes.
Now you are inside the chrome directory where you can find the configuration file "google-chrome" which contains the settings for chrome.
This file can be edited with any text editing software available in your LINUX distro. Let me use "gedit" to do this.
(Remember you need have administrator privileges which can be obtained by a "sudo" command)
Step 4: type "sudo gedit google-chrome" without quotes.
You will be prompted for the admin password, enter it.
The "gedit" text editing window will look like the snap-shot below
Step 5: Add "--incognito" to the last line of the text (see the snap-shot), save the file, close "gedit" and close the terminal. You're done !!
Open Google Chrome from the applications (or favorites) to see an incognito window opened.
In other words you've just made Google Chrome incognito by default. :)