Actually actually, with their swarm missiles, Basilisks have killed more mission critical cruisers, transports, and escape pods than about anything else.
Sure, if you let them, but given a half-decent primary and a few tempests you can get rid of a wing of them in no time at all.
Well, I think the problem is that a lot of people don't realize (at first) that they're actually pretty dangerous to vessels you're escorting. Hornets kind of suck, so you look at Basilisks and go, "Meh, they're just firing Hornets. I have more important things to deal w...what the ****? Where did that transport go?"

At least, I remember that being an issue for me when I first played Freespace 1.
In response to the OP question: @#$% Dragons.