There are a lot of ways to solve the problem that if the USB cable is plugged in, the display is on and fan is running.

One solution ist the following:

Remove the ARD_PWR jumper near the electronics fan socket.
The downside is: You cannot run your Ultimaker without an USB cable anymore (even if you try to print from SDCARD) because the Arduino is no longer powered by the external power supply (but from the USB cable).

Another is described here:

ultimaker.com/en/community/view/6131-disabling-usb-power-because-my-memory-is-crap
It works! But you have to desolder the polyfuse and solder a bridge. Looks like a mess in my eyes.

My solution is to simply desolder the MOSFET that is used as an switch to supply the USB voltage (+5V) to the arduino. You can see a picture above, just desolder the little device with the three pins that was in the red circle. You can take a look at the other pictures to understand why that works ;)

In order to get access to this part, you have to remove the fan on the electronics and then disassemble the Ultimaker shield from the Arduino (just pull it off). Please be very very careful while desolding (you can easily damage your hardware). A good idea is to cover the electronics with capton-foil and cut a little hole for the MOSFET. You can easily desolder it with hot-air this way.