It seems transporting can be stopped trivially easily, and indeed transporting will generally fail unless the circumstances are atypically favorable.
At least when it comes to starship transporters, that is. "Realm of Fear" suggests that transporters are in widespread use elsewhere as well, but there might be a crucial difference there - such as the one between cross-country racing cars and trams today. The "civilian" transporters might be hardwired systems where the phased matter stream never has to endure the hardships a stream sent from a starship across vacuum and atmosphere into a planetary surface has to. Such systems, unlike starship transporters, would be useless for stealing the neighbor's poodle and replacing it with fifty pounds of firecrackers.
Sure, we have seen that with a bit of training, a miscreant can build a transporter of his own, out of a common food replicator ("Visionary"). But the paranoid citizen might purchase all sorts of technologies established on screen, such as transporter jammers (low-level shields or whatnot that will bounce back the mischievous trespasser) or, if he wants to be nasty, scramblers (the kid that tries to beam in will rematerialize as mincemeat).