It's not a part of the OP's question, but what's available to use really comes down to economics. Which is more economical to use? Within Trek, the extensive use of hovercars and shuttles says to me that it's not always economical (or even efficient) to use the transporter. That, plus Sisko's line about transporter credits in "Explorers" suggests that transporter usage is a limited commodity for some reason. Maybe it takes far too much energy compared to a hovercraft or shuttle, maybe it uses up some other unrenewable resource, who knows?