Help me understand what's going on with the reset circuit in this simulation.

I also see no action on the diode. It seems to do nothing.

The purpose of the diode is to simply clamp any voltage applied to the reset pin above +5 vdc as can happen with the way the auto-reset functions that the arduino IDE used to force a reset to the AVR chip before uploading new sketch. The diode was added to the Uno rev3 boards after this reset 'bug' was finally understood and could be demonstrated. It was a subtle bug but the diode fixed it.