One of the main driving forces in Star Trek is an idea of tolerance of religious beliefs. This often comes in the form stating very blandly, "I respect your religious beliefs". Yet, one major complaint about Star Trek is its heavy view of secular humanism as a utopian-like future of most of human society. With strong atheists vehemently opposed to religion and secularist often unwilling to follow or deeply consider the religious beliefs of another, one has to wonder what it really means to "respect your religious beliefs".
With enough consideration, the answer seems more clear. One tenant that most people follow is an understanding that certain beliefs are rather axiomatic. That is, the foundation of one's belief structure is based more on one has learned than what is deduced. A firm rigidity to those axioms can, at time, lead to willful ignorance of reality. Yet, as open as many people claim to be, without some underlying basis to understand things, it is difficult if not impossible to organize or believe anything.
People, however, generally aren't so rigid as to be beyond change. As time progresses, generations of people come in contact with more people and more ideas and have to further evaluate the teachings of their ancestors. So, the axioms of one's fore bearers or even one's youth are at times called into question and generally evaluated not only with one's own other axioms but also with the axioms of others. It is through this that people can grow and change and tolerate others.
In the end, however, people have different axioms. The set of axioms may be better shared today than in the past, but people need a firmness in their own axioms to make decisions for themselves. To that end, a respect in another's religious beliefs is not a direct acceptance of another's beliefs. It is a respect that one must have some sort of underlying beliefs to exist and that it is unreasonable to expect or demand another to give them all up to tryout another belief system.
In short, it is not "I respect your religious beliefs". It is "I respect that you respect your religious beliefs". So long as the former is merely meant as a shorthand of the latter, they're equivalent. But, otherwise, the distinction is of significant importance.