Habermas criticises the version of compatibilism that is based on the idea of a “non-aggression pact between neuroscience and common sense.”* This seems to me a brilliant and accurate formulation. If by compatibilism we imply an uneasy co existence of two ultimately incompatible paradigms or visions then this is not what Habermas is aiming at. Habermas aims rather at “a genuine reconciliation of Kant and Darwin.” Kant here stands for “freedom” while Darwin stands for “limits.” Habermas in other words is not just content to show the “compatibility” of freedom and “limits,” he is rather aiming at something more positive, a genuine reconciliation of what is thought of as the realm of freedom and what is normally thought of as the realm of non freedom or even un-freedom.
The difference between the two approaches is roughly this: the compatibilist approach sees the relation between the realm of freedom and that of non freedom as that of negativity; the reconciliation approach on the other hand sees the relation in positive terms. As I have argued previously this involves abandoning a notion of freedom that sees freedom as essentially transgression of the “limits.” The second approach on the other hand sees the "limits" as the conditions of the possibility of freedom and not merely a transgression of the "limits."
Joel Anderson says that Habermas’ critique of compatibilism is not that the cost of accepting its truth is too high. Similarly Habermas’ critique is not that the truth of determinism is inconceivable. Habermas’ basic claims are rather a Kantian one: We can understand the “first person perspective” only performatively and that “not everything can be treated as object.” Moreover, the first person perspective or subjectivity is the necessary conditions “for engaging in the sort of activity that supports our sense of having free agency.”
This shows that Habermas’ main concern is rather different from the traditional concern of compatibilism. Habermas is not really concerned about the existence or non existence of freedom or with the question whether freedom can co exist with non freedom or even unfreedom. These are only secondary concerns for Habermas. Habermas’ main concern is how the Kantian notion of subjectivity can be genuinely reconciled and defended within an overall naturalistic (in the sense of weak naturalism)
* Joel Anderson, "Free will, neuroscience, and the participant perspective." All quotations in this post are from this paper.