I see transporting as like this. * A transportee is transported out of the conventional universe * A transportee travels through a subspace corridor * A transportee reenters the conventional universe (On a transporter console aboard the Enterprise-D, there are controls for the subspace field compensation. See here - http://tng.trekcore.com/hd/albums/1x06/wherenoone_hd_018.jpg) I feel there are safeguards on at least one of the 'portals', which is used to weed out biological contaminants. or to disable weapons. As long as the cargo is secured, there is no danger to the crew or to the ship.