I've never been convinced. I assume that the matter stream is actually transferred by subspace or similar, hence they can beam inside of buildings. How do the scanners work to a molecular, let alone quantum, level, at a distance of thousands of km?
Of course it doesn't really make sense, but it makes more sense than the old "matter-to-energy" idea. A single gram of matter contains about as much energy as was released by the Hiroshima bomb. Converting a 70-kg human to energy and firing that energy at a planet would basically be a WMD attack.