A honest yearning for the truth might resemble zealotry in it's intensity, but it is another thing entirely from the type of zealotry that often springs out of nonsense, like religion.
Well that's the thing. for some it isn't an honest yearning, it is the same arrogant assumption of being completely right.
As for the difference I don't think in this case there was any difference in the bullets that sprang out of the gun, just because they were fired by someone who thought he was fighting for atheist equality.
(edit)
For that matter, it begs the question of what rational thinking and evidence Sam Harris is using when he says something like this:
"While the other major world religions have been fertile sources of intolerance, it is clear that the doctrine of Islam poses unique problems for the emergence of a global civilization."
"It should be of particular concern to us that the beliefs of devout Muslims pose a special problem for nuclear deterrence."