First of all, in this aspect, we were talking about the concept or idea of religion.
Now, despite feeling like the idea of religion is bogus, i can accept that people that im surrounded with are in fact religious and feel the urge to pray or whatever. I do that, because it doesnt affect me or any other one in any negative way. If i wouldnt feel that way, and maybe feel like there is some threat for me coming from religious people, i wouldnt be able to accept this circumstance and i would try to fight it.
However, i will never ever show respect to the idea/concept of religion. I cant respect something that i feel is totally wrong, backwards, stupid, whatever.
At the same time, this doesnt mean that i wont have respect for the person. This is all about the question "is he or she a good person?". Lets leave the question beside what is good and whats not.