Electronic – Digital oscilloscope maximum input voltage

It looks like the test is designed to be done as a loopback test (i.e. with the SIMO/SOMI pin shorted)
If you don't have them shorted, you won't see anything on the SIMO line unless you have a signal input from elsewhere.
SIMO = Slave In Master Out
SOMI = Slave Out Master In
I'm assuming the beagleboard sets itself up as a SPI slave, hence the pin names (more commonly MISO and MOSI)

As far as the scope settings go, x10 for the probe is best as it adds the lowest capacitance load to the line under test (means you can see higher frequencies)

For the timebase and Vdiv, just set things up as needed on the fly. 2us and 1V/div sounds fine to start with. You would often set the Vdiv to a sensible value for the bus voltage to get the signal to fill a large portion of the screen.

Then adjust the timebase in/out when you want to focus on different things, e.g. smaller if you want to check the risetime of the signal, ringing or transients, larger if you want to see more than one byte or stuff like power supply interference.
You will quickly find you are twiddling the knobs constantly when debugging, so don't worry too much about initial settings.

@Tom Carpenter's comment is correct. All oscilloscopes are "mains-Earth" grounded. Which means that the ground lead is connected to the ground pin of it's power plug. So what you actually did was this:

The ground lead always must be connected to the actual ground of the circuit under test when using an oscilloscope.*

*Unless you use an isolation transformer on the device under test, with NO chassis or Earth ground.

Also what Tom means by "making the oscilloscope do subtraction" is to connect two channels across the resistor, and grounds to actual ground. On the display will be two waveforms. Enter the "math" function of the oscilloscope, and instruct it to subtract channel 2 from channel 1. The result will be the difference between the two, which is the voltage across the resistor.