One thing that really annoys me is the conflation of religion with religious people. It's a common and dishonest defense of religion to claim that any criticism of dogma and superstition is an attack on 90% of the people on the planet — it's like ducking and hiding behind 5.5 billion people and making the argument from authority and the argument from popularity all at once.
Now, I entirely agree with P.Z. on this point. But it's interesting to note the (formal) parallel with that Christian favourite: "love the sinner, hate the sin." For us militant atheists, it becomes something more like "love the religious, hate the religion." This parallel raises some interesting challenges for both sides.
Firstly, it makes one wonder why Christians are so prone to the conflation. If the sinner/sin distinction is so important and familiar to them, why do they have so much trouble recognizing it when they're on the receiving end? Very puzzling.
As for atheists, well, it really should give us pause. We can't stand that "love the sinner" nonsense -- we typically think it's an insincere excuse from homophobes who don't want to admit their bigotry. Or, even if sincere, how can you genuinely respect (let alone "love") a person when you reject a central aspect of their "personal identity" (in the pop-psychological, not philosophical, sense)?
The difficulty here is that for some people, their religion is as centrally important in their lives as their sexuality. So if we hold that disrespecting homosexuality means disrespecting gay people, then aren't we also committed to holding that disrespecting Christianity means disrespecting Christians? I can't see any relevant formal difference that would allow me to deny this implication. But note that this applies not just to Christianity, but any beliefs that an individual cares deeply about. Astrology and other "new age" rubbish springs to mind - as do political ideologies like communism, Nazism, etc.
This presents us with four options. (1) We could try to have more respect for all the idiotic and pernicious belief systems in the world. I'm not too tempted by this one, you can probably tell. (2) We could deny that anyone is being disrespected after all. This would force us to respond more favourably towards (sincere) usages of the "love the sinner" slogan. (3) We could judge that the "disrespect" involved, though real, is justified (in both cases) by its role in public dialogue about values. This has similar practical implications to #2 above. (4) We could deny the parallel on substantive (rather than formal) grounds. That is, looking at the actual content of the claims being made, it happens that our position is justified and theirs isn't.
So... which is the best option?