What you have to realize about the transporter was that it a was, in a way, a "necessary evil" at the time the show was produced. They needed a way to get their protagonists to and fro from ship and planet, and didn't have the budget(at first) for making and filming a shuttle craft. (The shuttle craft wasn't introduced until its existence was integral to the plot of the episode.). As a plot device for getting to the meat of the story quickly it was perfect. One drawback in story terms was that now they had to keep coming up with reasons why our heroes couldn't just thumb their noses and beam back up to the ship every time they got in trouble.