Easy anticheat needs to be disabled for the trainer to work.
How to disable Easy Anticheat: Uplay
Go to Game Properties in Uplay and click on Edit next to game launch arguments. Enter -eac_launcher and click Save.
With version 1.07, you need to add the command to steam too.
How to add command line argument to steam
Right click on game in steam and go to Properties. Click Set Launch Options. Enter -eac_launcher and click OK.
You should get this message in game if EAC is disabled successfully
You may need to restart your PC to unload the service if it isn’t disabling after doing all that^.
Thanks to cheathappens/dr8breed for sharing how to disable EAC.
Note: With new versions now you have to launch it from a shortcut.
Make a watch dogs 2 shortcut then add the -eac_launcher command line parameter to your WatchDogs2.exe shortcut.