One cause of such skepticism, I suspect, is that some of the canonical cases Kripke adduces in Naming and Necessity are not particularly clear cases. That is, they are borderline or disputable cases. In addition, the attitude Kripke seems to take to these cases may not be completely appropriate. With these cases, he sometimes gives the impression that the way to know how it is with them is to use intuition - and here the intuiting has a different character than in clear cases. It seems like a kind of hearkening or special receptivity is supposed to be needed. All this may seem, so to speak, occult. And if this doesn't put us off the notion altogether, it may yet mislead us about what sort of account we should look to give of it.
The sorts of cases I have in mind are those of the table - could it have been made of ice? (Kripke intuits that it couldn't.) And the Queen: could she have been born of different parents? (Kripke intuits that she couldn't.)
(One thing about the Queen case which has troubled me for years is what I call the fish argument. This argument works by iterating the supposed necessity of origin; if the Queen is necessarily the child of her actual parents, and they are necessarily the children of their parents, then we seem to be forced to conclude that the Queen is necessarily the descendant of some fish which she is in fact descended from - call him Colin. That is, there is no possible world involving the Queen where Colin isn't also around. This seems dubious.)
To all this, my suggestion is that we shouldn't get hung up on such cases when it comes to the question of whether the notions of metaphysical or subjunctive modality are legitimate, and when it comes to understanding those notions. Just as, when trying to give someone a grasp of the notion of tallness, it is better to work with examples of people who are definitely tall, or definitely not tall. To start insisting on certain judgements about more borderline cases is not to the point, and may make the whole business seem dubious. I think that following my suggestion may help us both explain and legitimate the notions in question, and may help us account for them in the proper way.