Modal accounts—and I take counterfactual ones to be a special case—typically do not get at the heart of what is going on. Consider for example the account of free will in terms of the Principle of Alternate Possibility (PAP), or the account of causation in terms of counterfactuals. Both fail, and in both cases there either are counterexamples or there are cases that are so close to being counterexamples that they significantly lower our confidence in the claim that there are no counterexamples. Yet PAP and the counterfactual account of causation do get something right. I think what is going on in both cases, and maybe in cases of other modal accounts, is that the account confuses explanans with explanandum (or, more fluently, cause with effect). It is because I am free that I typically have alternate possibilities, and it is because A caused B that were B not to have occurred, A would not occur.
Typically, explanatory and causal relations can be blocked—the explanans can be had without the explanandum. So one can have A causing B without the counterfactual, and one can have freedom without alternate possibilities. But these are not going to be standard cases. Now if causal determinism of the standard variety were generally true, then surely we would not be the possessors of a faculty innately capable, in the right external circumstances, of producing events with alternate possibilities. And so we would not be free. So an argument from PAP to indeterminism can still be made, despite counterexamples to PAP.
Modal or counterfactual stories like PAP may show that a view—say, compatibilism—is false, but they typically fail to get at the essence of why the view is wrong. (When an argument against a view is given that fails to get at the essence of what is wrong with the view, it can trigger a large literature of attempts to tweak the view, nitpick about problems with the argument, etc.) Here's another example. The knowability paradox argument against anti-realism. From the claim that everything can be known by beings like us, we can prove the absurdity that everything is known by beings like us (just apply the claim that everything can be known by beings like us to the proposition that p is an unknown truth). This is a perfectly good argument, but it fails to get at the essence of what is wrong with anti-realism, and that is a part of why instead of being simply taken as a perfectly good argument as it should be, it is taken to be a paradox.