Swapping Apple and Ctrl Keys

In the terminal enter:

cat > ~/.xmodmaprc
! Erase existing bindings
clear Control
clear Mod4
! Map key 37 (left ctrl) to Super_L (i.e. 'cmd')
keycode  37 = Super_L
! Map key 133 (left cmd) to Control_L (i.e. 'ctrl')
keycode 133 = Control_L
! And update modifier settings
add control = Control_L
add mod4    = Super_L

Press ctrl+c to stop editing the file and log out and in. Upon login Gnome will ask to accept the .xmodmaprc file. Click on the load button. Done.

other option

Go to system settings > keyboard > layout settings > options > alt/win behaviour and select 'Control is mapped to Win key (and the usual Ctrl keys)'. Now shortscuts like ctrl+c will work with both the ctrl AND the cmd key. You will lose your super key, but I never missed it.