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?
Just as a matter of concept: for a variety of reasons, no new invention ever fully replaces an old one. The biggest reason for that is that the original invention often benefits from the new technology and manages to stay competitive in either case.
You wouldn't abandon vehicular traffic because transporters exist; quite the contrary, vehicle manufacturers would find ways to use transporters to make their businesses much more profitable, either by equipping their vehicles with short-range transporters (as a safety or convenience feature) or making the vehicles transporter-compatible so you can sit in your car and have the whole thing beamed to Pittsburgh where you spend the entire day flying around the skyline inspecting holographic billboards for FCC compliance. Your hovercar would be that much cheaper and more efficient since it doesn't ITSELF need to have enough power to fly to Pittsburgh.