The problem with making long-distance transporting routine in the Star Trek universe is that it renders the entire format of Star Trek obsolete. If you have interstellar beaming, what do you need starships for?
Transporters have always been a plot device with the potential to be far, far too powerful to be good for the story -- in principle, they could get characters out of any crisis easily, allow resurrecting the dead or healing any disease or injury on a regular basis, they could create an army of clones of a person, etc. So ST has always had to impose limits on what transporters could do, in order to keep them from compromising the storytelling: they can't beam through shields, they can be blocked by certain materials or radiation types, they have memory limitations that won't let them permanently store enough data to replicate a live person, etc. Writing about transporters has always been a tricky balance between giving them the abilities they need to drive the story and keeping enough limitations on them that those abilities don't upend the whole universe. Since Bad Robot is new in the Trek game, maybe they haven't quite gotten the hang of that balancing act, so they exploited the convenience of long-distance transporters without thinking through the long-term ramifications and the need to impose limits on them (so it's fortunate that TNG: "Bloodlines" already gave us a handy set of limits on the equivalent technology).
The alternative is to embrace those godlike powers of teleportation and actually build a universe around exploring their ramifications. Novelist Wil McCarthy had an interesting take on that in his Queendom of Sol tetralogy. But that would be a rather different universe than the one Star Trek has always been about.
Well remember what Scotty said in the story:
I take this as that maybe somebody could cut off a relay or stop re-materialization (actually killing or destroying the subject). So that I believe is the limitations imposed. Sure it's fast, but even the slightest mistake can be positively deadly, a ship is far safer and even more versatile in many situations..