Lets not stretch the metaphor to far... of course it will break down under detailed scrutiny. The parallel here is simply that the high level principles are similar, and hence why should the other side view the others point of view with such disdain.
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Perhaps disdain is unfortunate. However, on one side you have people who believe that their beliefs determine whether or not they spend eternity in heaven or in hell; and they are also tasked with sending as many people as they can to heaven by instilling correct knowledge. This task too determines whether they go to heaven or to hell. These people, then, are very motivated to be antagonistic toward ideas that conflict with their mission. And, based on their premises, rightly so. In fact, I think they should be much more antagonistic to those ideas.
On the other side - the non-theists - you have people who do not have a belief in a god or godly things. It would not make sense for them to grant any intellectual validity to ideas that are anchored in such things. No more than you would grant intellectual validity to a child's belief that Santa will pass him by because he has no chimney. Should we feel "disdain" for this child? Perhaps not. But we should certainly feel disdain for the belief. Or, if not disdain, it would at least be immoral and unintelligent to grant it any benefit of doubt. The only time we should reconsider is if the child grows up, goes exploring the North Pole, and finds a warehouse of elves making toys.
:)