The dangers of microwave radiation, much like the dangers of cell phone and other non-ionizing forms of radiation, have absolutely no basis in scientific fact. Microwave radiation can't change the molecular structure of anything, because it simply doesn't have enough energy to break apart chemical bonds.
To put it in perspective, plain old visible blue light has many, many times the energy of a microwave, and can break apart weak chemical bonds (this is what causes photochemical smog).
Microwaves actually have less energy than the infrared radiation (i.e. heat) that is given off by our bodies and the earth.