In the past few decades, many empirically-bent workers in cognitive science, psychology, and philosophy have taken it upon themselves to correct our illusion that we have free, conscious will. The problem that many of these theorists overlook, however, is that the idea of free will can be separated into two relatively independent processes, differentiated by their respective time scales: short and long.
Short term physical activities are largely concerned with constructing the appropriate movements to match the current situation, like picking up and writing with your pencil, or walking down a street—both of which require incredibly complex movements from a basic systems level. The nature of our nervous system, however, allows such movements to be written into the system itself, such that the resulting structure of the system allows these movements to take place with little information processing needing to be done.
Correspondingly, in the realm of the brain, both empirical and theoretical viewpoints do, indeed, point to a remarkably diminished activity of free will—one need only think of split-second decisions as an example. A great many of these split-second decisions turn out differently than we would have preferred, given a chance to deliberate. This side of the issue makes sense from a biological/organismal standpoint: If we have incredibly complex brains that are capable of a great deal of things without conscious attention, why not take advantage of that when it comes to basic mental events? In this way, short term mental events and short term physical events are not so different. Such a method of functioning allows more resources to be devoted to other higher-order matters of cognition, such as planning and deliberation.
Planning ahead and considering possible alternatives is where the long term variety of conscious will starts to play a significant role. Planning and deliberation are not merely a system of inputs onto your nervous system with a more or less pre-set outcome, as is the case in many short-term scenarios. It involves assignment of value to certain outcomes, and a subsequent weighing of those values against one another. Note that I am not trying to say that long-term planning is not ultimately a result of physical actions in the brain, but rather that it is not so simple as its short-term counterpart. I am also not saying that these two time-scales are fully separate—if I were, then the long-term system could not influence the short-term system and people could not be help responsible for their actions. My view is instead that long-term systems work to influence and entrain the short-term systems towards a desired pattern of outputs. The details of this system need to be worked out, but the cursory description lines up more closely with experience than the one outlined at the top of the article.
The problem with those who use currently available empirical data to undermine free will, then, can be summed up quite simply. All of their data is built around short-term decisions. But even advocates of free, conscious will see reason to doubt short-term decisions as being fully controlled by consciousness. So, in effect, the present researchers are merely proving something true that most experts already thought true. The only objection to them, is this: short-term data do not reveal much of anything about long-term phenomenon. For a clearer example, the composition of a small pile of sand on a beach does not reveal much about the grander process of tidal erosion.