A microwave oven functions by dielectric heating of water molecules and other polar compounds, usually proteins in food. The alternating electric field of the microwave radiation, commonly at a frequency of 2.45 GHz, causes rapid reorientation of the polar molecules, generating heat by frictional interactions with neighboring molecules. The water molecules are highly magnified relative to the large organic molecules for better visualization of their oscillations. The microwave oven turns itself off when the contents are sufficiently heated. Doesn't that protein molecule look yummy!
For more information, see the Wikipedia entry for "Microwave oven".