VOY exploited this transporter weakness with the Borg on two occasions.
Once in 'Dark Frontier' to destroy that small scout ship, and the second time in the episode with the Brunali where they returned Icheb to his home planet (they beamed a photon torpedo onto the sphere just as it dropped its shields to pull VOY inside it and dealt moderate/crippling damage to the Sphere).
It makes sense you could do that with the Borg once or twice, but not past that point... plus, the passage of time between those two events was over a year if I'm not mistaken.
Usually, shields offer a good protection against transporters, unless you can match the frequencies which would allow the beaming signal to penetrate it - we have evidence that shields CAN allow transporter signals if you know the frequencies... but lack of inhibitors never made sense during red alert.
Then again, remember that initially, 24th century SF ships were portrayed as having a smart computer system which would also encase intruders inside a forcefield at ANY section.... this ability was progressively seen less and less until it was apparently 'phased out' and things were done either manually, or a new system had to be built to do this (why? its already there).
I'm thinking the writers are conveniently forgetting these technologies for the purpose of 'drama' (even though they should instead adapt the story to FIT with the technology and work with what is established - it doesn't need to take away from the experience at all, just make the story smarter - and of course, if the ship becomes damaged enough, you CAN get away with some of these technological advantages - but as we saw, SF ships can apparrently project forcefields across LARGE missing sections of the hull that was lost in combat even if a ship is heavily damaged).