Are some theists afraid of atheists?

[The Grand Nudger]

Okay, I will refrain from critique of your position in this post and ask only that you do me the favor of clarifying your position on certain points. However, I will quote your post out of order for the purpose of enhancing what I believe is your line of reasoning.

What is being leveraged and what is providing the leverage? I take it that, for you, a moral schema (framework for thinking ethically) starts with feelings of empathy and proceeds by applying reason to determine how people should act on those feelings. Is that correct?

Not even remotely.  My moral schema is a series of propositions regarding morality, beginning with moral facts of a matter. I'm simply pointing out inoperable objections to some other moral schema as you provide them. That, even ignoring the basic failure of your objections...reasoning from empathy (nor empathy itself) does not necessarily satisfy your own description of an instrumental good...though I'm sure it could, in some instance, just as moral reasoning could, in some instance - and just as many "value by decree" systems invariably and necessarily -do-. Nor, for that matter, would it matter if they did, as the only problem in that is created by yourself, in insisting that human dignity not be contigent when..by any rational use of the word, it will be contingent on something. If, however, we maintain your own assertion then it would simply mean that we do not posess the kind of morality that would satisfy your assertions.....we still, however, posess a morality. That doesn;t change based upon your dissatisfaction with it or the errors people have made in describing it.

Based on my understanding above, this means that people reason from feelings of empathy to estimate what would maximize personal benefit.

Your understanding, above, is a convenient fiction whose only purpose is to serve your objections, and flies in the face of any instance in which a person does reason from feelings of empathy in ways that are not even remotely concerned with their personal benefit, or flatly in contradiction to it.   Helping a shady drifter on a cold night is undoubtedly empathetic.......but probably not a very good way to maximize personal benefit, agreed?

Some evolved traits that may have ceased to provide a reproductive advantage or may now ill-adapted to civilized societies. Similarly some traits may opportunistically confer advantages to a species in response to changes in environment.

I’m not sure why you think these facts are relevant.

The fact that I think is relevant, that you quoted but did not opine upon, is that both our empathetic apparatus -and- our rational apparatus evolved for "some other purpose".  Chiefly, finding food and avoiding being food.  That's not what we use either for anymore, nor does it it fully categorize all uses thereof.  IOW, the evolved objection form instrumental goods is a toothless objection, as you attempt to leverage your evolved rational apparatus to somehow rule out some other evolved apparatus' validity or utility.  They can both be validly used to great effect, if the subject is morality.  They can both be used to ground a moral system, rationally - though obviously I think that moral reasoning from facts of a matter is more robust and concrete than moral intuition..empathy.....though the best use of both, imo, is a complimentary one not at all concerned with finding food or avoiding being food.  

I don’t think you will find anything to the effect of “sometimes it doesn’t work” in my demonstration. Is there a specific premise to which you are referring? Also you seem to be saying that people sometimes make bad choices. True, but I do not see the significance. The demonstration only concerns itself with whether or not reliance on empathy is a truly rational ground for an ethical system. What am I missing?

The demonstration doesn't concern itself with that at all, if we're being blunt, and isn't even a demonstration.  It's a string of assertions divorced from any factual appraisal of any of the particulars to which it objects meant to gouge a hole where there is none... into which you will invariably plug your silly god.   / shrugs. 

So are you in essence making the following argument?:

I value my own life.
I am a human being.
Therefore, I value at least one human being.
Other people are human beings like me.
Therefore, I value other people.

More like

I value my life for x
Others satisfy x
Therefore they have whatever value I've assigned myself for the same reasons that I have assigned myself this value.

A person who start with their moral intuition can get simpler with what they then leverage to manifest human dignity in the world;

Being punched sucks
Therefore I shouldn't punch people.

So are you in essence making the following argument?:

I am a human with emotions.
Some of my emotions feel bad.
Other people are humans and it is reasonable to infer that they have emotions, just like me, some of which feel bad.
I have knowledge of what makes me feel bad.
Therefore, given basic epistemological limits, I have knowledge of what makes other people feel bad.

No, I base my moral schema off of harm, -the moral fact of the matter.; so

I can be harmed.
When I am harmed it causes me pain
Other people are human beings that can be harmed and it is reasonable to infer that they too feel pain
I have knowledge of what harms me and makes me feel pain.
Therefore, given basic epistemological limits, I have knowledge of what will harm others and make them feel pain.

From there I’m not entirely clear on how you would link what I presume are your two main lines of reasoning into a single coherent argument. I think you are trying to say something along the lines that you value not feeling bad and therefore you should value not making other people feel bad. Or something like that.

I hope I cleared things up for you with regards to my own moral system.  Rational self interest does, however, posit that you should not do to another what you would not have done to yourself if...for whatever reason, you're the kind of asshole who constantly finds himself wishing to harm others and cannot be swayed by any other motivation.