How do I switch the Command key and Control key on a MacBook Pro?

I figured it out. Put the following in ~/.Xmodmap:

clear control
clear mod4

keycode 105 =
keycode 206 =

keycode 133 = Control_L NoSymbol Control_L
keycode 134 = Control_R NoSymbol Control_R
keycode 37 = Super_L NoSymbol Super_L

add control = Control_L
add control = Control_R
add mod4 = Super_L

To test, run the command:

xmodmap ~/.Xmodmap

To make it run every time, add it to Startup Applications.

This should work on any MacBook Pro; the issue was that Xmodmap was assigning Super_L to the left and right command keys, and Control_L to the left control key. For some reason, by default, Ubuntu thinks that the MacBook Pro has a standard 105 key keyboard (probably thinking about the full Apple Keyboard) but that is wrong. Anyway, I reassigned the keycodes to the right keysims, then assigned the keysims to control and mod4.

I just installed Ubuntu 16.04 dual boot on my MBP13" yesterday. For Ubuntu 16.04, here's how i did it:

Step 1: Launch terminal

Step 2: Edit X Keyboard Extension

sudo nano /usr/share/X11/xkb/symbols/pc

Step 3: Make the following changes. Ensure your file looks like this:

key <LCTL> {    [ Super_L       ]   };
key <LWIN> {    [ Control_L     ]   };

...

key <RCTL> {    [ Super_R       ]   };
key <RWIN> {    [ Control_R     ]   };

Step 4: Clear xkb's cache

sudo rm -rf /var/lib/xkb/*

Step 5 (conditional): If the keys are not swapped after step 4, restart your computer. It worked for me after this.

Hope it helps, good luck!

Go into System -> Preferences -> Keyboard

Click on the "Layouts" tab and then click the "Layout Options" button.

Click on "Alt/Win key behavior"

Select "Control is mapped to Win keys (and the usual ctrl key).

from http://ubuntuforums.org/showthread.php?t=1293081