My initial hypothesis was that there's a theism bias.
An earlier question noted that philosophy of religion has a theist majority.
If we look at your one link, we can see that's indeed the case:
| r: 0.45 |
God: theism |
|
| Free will: libertarianism |
Accept |
Reject |
| Accept |
167 |
134 |
| Reject |
147 |
1083 |
A mere 11% of atheists accept libertarianism, whereas 53% of theists accept libertarianism.
This may not fully account for the difference (it would seem pretty close to 54%, but 20% of philosophers of religion are atheists, which drags the number down). But it seems fair to say that this has the biggest effect, and the remaining difference may be more subject to noise.
Why is there a theism bias?
Well, theists commonly accept that there's something "outside the physical"* (whatever that means), that there's at least one consciousness (a god or gods) not subject to "physical" (typically deterministic, or random) forces.
* There's a strong correlation between theism and rejecting physicalism - 94% of theists reject physicalism (806/(53 + 806)).
It's also a fairly common theist belief that human consciousness persists after death.
So it's not much of a stretch for them to think human action is not subject to deterministic forces, i.e. libertarianism.
As for why 47% of theists (and 89% of atheists) reject libertarianism, one might suspect that they see too much evidence that makes them think our actions are subject to deterministic forces, in the form of neuroscience, psychology and evolution, or they find libertarianism to be incoherent. For theists, this may overwhelm their theism bias, whereas atheists don't have theism pushing in the other direction. But this is much more speculative and based on my own views on the matter. It might also be that non-libertarian theists reject libertarianism exactly because of their god belief, i.e. God determines every event (as per user80226's link).