1) Teleporters screwing up is one of the most common trope as there's numerous things, that can go wrong, you'll get teleported during April shower and you could end up in mirror universe.
2) Whole process must be quite costly (and used to be restricted via credits during TND/DS9 era, where it was much more common and used by common citizens... at lest on Earth and other "core" planets) and that cost will be paid separately for each person.
3) BOTH those numbers (chance of teleport disaster and energy requirements) will go up but energy required to transport 1 or 10 people with shuttle will remain more or less same and shouldn't really make it more difficult for pilot unless he's in middle of warzone or natural disaster.
4) It might be a form or relaxation for individuals to chill before important meeting or catch up on intel as well as ST equivalent of recreational driving.
5) Story pacing still plays major role in all of this. Shuttle scenes give you relative peace to hold various discussions, either for character development or exposition, in relative peace and can also provide more "will they make it" kind of drama. TOS introduced teleporters because shuttles were more expensive to shoot and while their budget was pretty big for it's time, you always have to cut corners on TV. So while there is a room for rationalization, it's mostly meta issue as unlimited teleport devices are way too convenient... or actually inconvenient as far as drama and thriller are concerned.