You make several points here, and I may not respond to all of them. But first, there may be any number of reasons why people regard non-human animals as not meriting the same degree of moral regard as human beings. I think (given the format of this site) it is probably best here simply to provide some basic indication of how this might be appropriate, so think of it in terms of how we value reciprocal relationships. We value our pets, in this way of thinking, because they really do reciprocate our attentions and affections--at least, as far as they are able to do so. But the reciprocation that is possible between human beings and their pets is limited--far more limited than the reciprocation that is possible between human beings. So it may not simply be a matter of valuing certain traits (e.g. intelligence) in a prejudicial way, so much as the ways in which such traits allow for richer (and more reciprocal) relationships.

As for religion's regard for non-human animals, it will really depend upon the religion. The religions of South and East Asia (Buddhism and Hinduism, for examples) tend to value animals more greatly than those with their roots in the Middle East (Judaism, Christianity, and Islam). Recall that in Genesis, we are told that God gave human beings dominion over non-human animals, with the implication that the other animals came into existed for our use (e.g. as food, or as beast of burden).