It is an important distinction worth reminding people about and I wonder whether I sometimes fall into the trap myself. Tolerating a belief means that you do not try to forcibly stop people from holding it. It is not the same as letting that belief go unchallenged. (That is where the respect comes in.)
For me, I think the real issue is over the boundary between religious beliefs and religious practices. Whilst there is a definite need to tolerate the former, there is no need to tolerate the latter. (One only has to imagine a religion that features ritual murder and cannabilism to see this.) As coelsblog says:
"Yes, religious beliefs should be tolerated, and, yes, religious practice should be tolerated (provided only that it complies with the usual civil law)..."One problem, I think, is that people often conflate refusal to tolerate certain religious practices that don't comply with civil law with refusal to tolerate religious belief, for they often see them as one and the same. So, the fact that Creationism is not tolerated in a science class (or the Giant's Causeway) is interpreted as a lack of tolerance for the religious belief behind it, whereas really it is the result of a lack of respect for that belief.
This is, in essence, the heart of secularism: people can believe what they want but it is up to society to determine what is acceptable behaviour and no belief system (religious or otherwise) gives one a "get out of jail free card" to ignore or supersede the laws, rights and responsiblities that follow.