To be a tad more constructive, the term “respect” has degraded in usage IMO. In this context, it really should be in the context of “I respectfully disagree”. It’s part of being civil–that is, we don’t call each other doody-heads when we disagree. If all people in a conversation can reason with clarity, there is room for debate, and room for multiple opinions. In order to function, we have to keep the discussion “respectful”.
That doesn’t mean that you hold someone’s beliefs in high-esteem, it means you don’t belittle him if you disagree.
Religious discussions are fundamentally impossible to conclude with pure logic and empirical investigation, because most modern belief systems don’t have falsifiable claims. For instance, I believe that Jesus Christ died and was resurrected–a most remarkable claim. It’s not something I can prove scientifically, but then I don’t propose it as science (nor am I a young-earth creationist for instance). I claim to have experienced revelation of the divine, and hence know for myself Christ’s divinity. When I share that with others, I don’t try to convince them, I merely present my experience and invite them to try to experience it themselves, and act on the results of that attempt. If he doesn’t have the same experience as I do, I don’t browbeat him into agreement. And if he isn’t interested in investigating what I believe, I don’t ridicule him for it (even though I think he’s missing something good and important). The simple fact that there is disagreement doesn’t indicate anything about mental capacity or anything of that nature.
For insance, noting Zagadka’s location, I’ll point to my UCB degree in CS and note that an institution he may respect seems to think I’m capable of thinking logically, irrespective of the sanity of Joseph Smith. 
In addition to being unproductive, it is dangerous to disregard those you disagree with. gobear for instance not only dismisses Libertarian in the referenced thread, he goes beyond that and makes a ludicrous assertion, namely that God doesn’t exist. And self-respecting thinking person should acknowledge that knowing such a fact is impossible. At best you can claim you don’t know, or that you don’t believe. But an open assertion that God doesn’t exist is simply indefensible.
It’s this lack of civility that I think is the single greatest danger to the world today. It’s the source of the incredibly partisan politics going on in the world, threatening to destabilize the civilized world. (The SDMB is a perfect microcosm of that world today–it’s the primary reason I hesitated in signing up for the new pay-system.)
