Why would microwave cooking be bad (for the food that is)? It doesn't ionize anything, it just causes water, fats, sugars, (and some other substances with dipoles) to rotate (called dielectric heating). This movement causes the item to heat up.
We're bombarded by microwaves all day from wireless networks, etc all day.
I agree with Beachbnny though, plastics (any plastics) and the microwave don't mix.