Well, Star Trek Rules state you can't transport or shoot through shields. If the baddies are shooting at you, chances are you have your shields up, so you can't transport.
If you're shooting at them, chances are they've got their shields up, so you're still screwed.
If the other ship is disabled to the point that their shields don't work, then you don't really need to worry about it anyway.
Besides....transporting creates tachyon fields, which are the root of all evil in the ST universe.
No joke, I was watching an episode of TNG 2 weeks ago, one that I had never seen and all this weird crap was going down and they couldn't figure out what it was.
I turned to my gf and was like "$10 says the problem is related to tachyons."
Sure enough near the end of the episode, Data's like "I got it! There's a tachyon field fuxing our crap up!"
ROFL.
When in doubt....tachyons.