Below I ramble about the Cylons as "machines." Colonial "machine" discourse assumes that "machine" is a stable term with one transparent meaning that allows non-machines to say, for example, "If X is a machine, it's subhuman." I'd argue that, on the contrary, what it means literally and morally to be a "machine" varies depending on your definition of one. Moreover, the definitions that could reasonably pertain to the Cylons do not strongly indicate their inferiority to humans. (No spoilers.)
The definitions below aren't dictionary definitions but usages I've encountered. (Colonial definitions may differ, but Colonial society seems so patterned on America, I bet they don't differ a lot.)
1) An object with at least semi-automated parts, created by (dare I say) the intelligent design of another being(s) of less greatness than God.
The important part of this usage for BSG is that a machine is created by someone else. Humans are the Cylons' creators (and, therefore, something like their God -- from the human point of view). If a machine, in this sense, is "inferior," it's because it's a secondary creation. The underlying assumption is that if you create it, you're entitled to control it. This, however, seems dubious for the same reason it's dubious to argue that a parent should have control of a (grown) child because the child is the parent's creation. Self-determination, by definition, arises from self, not social/reproductive relationships.
2) As above but specifically made of inorganic materials or compiled from scratch out of basic constituents (as opposed to genetically engineered species, for example).
This would apply to the old-school Cylons but clearly doesn't apply to the new ones, who do seem to be largely beings genetically engineered from humans. (They must be genetically very close to humans if they can interbreed with them.)
3) An object that functions according to mechanistic principles, i.e. that has autonomic functions based on set laws.
This is what Descartes meant when he called animals "machines." The traditionally corollary is that a machine is not conscious and its functioning is purely automatic (so Descartes thought of animals). Colonial society does not seem to regard the Cylons in this light: it's generally assumed that they can make conscious decisions... And yet, Descartes's value judgment -- we can do what we want to animals because they aren't conscious -- seems to be tacit in a lot of Colonial attitudes toward the Cylons: it's okay to torture them, for example. But perhaps "consciousness" per se isn't the issue.
Traditionally, this definition has opposed "machine" to "soul." Animals are machines, says Descartes, because they are body without soul. So, too, Descartes says, are human bodies machines separate from the soul that is the true essence of humanity. So, too, does Kara suggest to Leoben that he's scared of dying because he worries that he doesn't have a soul -- and he doesn't have a soul because he's just a machine, a program.
A problem with this dualistic approach is that it assumes that selfhood does not derive from a physical substrate. Our selfhood is defined by our souls, not our brains, not the biological "machine" part of us. While this idea worked for Descartes in the 17th century, more modern science keeps throwing kinks in it. We see people change as a result of brain injuries. We see a clear correlation between brain structure and behavior in humans vs. other animals. And in Colonial society, they're faced with real "AIs," beings that aren't supposed to have "souls" yet clearly have brains and consciousness that function very, very similarly to humans'. This reduces the "you are a machine, so you have no soul" argument quite literally to an article of faith. There is no empirical evidence of any radical difference between human and Cylon minds/states of being. Cultural differences, certainly -- and maybe even some behavioral differences that are innate (perhaps a certain Cylon selfishness?). But even if that's so, the observable behavioral difference between human and Cylon is no greater than variations we can see within the human race: between Adama, Cain, and Helo, for example.
4) An entity that is divorced from "normal" feelings and moral responses as in, "He's more machine than man now, twisted and evil."
This definition is purely value judgment: if you're cold and immoral, you're a machine. Really, this is a metaphor arising from definition 3 ( you're "soulless") rather than an actual, physical definition. (What defines Vader as "more machine," for example, is not his "mechanical" bits but his fall to the Dark Side.) The Cylons (or many/most of them?) could certainly fit this definition "from a certain point of view" [sorry, once you start, you can't stop] but not because they're categorically different from humans. Cain would fit this definition too, just as Vader does. Conversely, Sharon seems not to.
As far as I can see, the argument that Cylons are inferior because they're machines cannot be developed beyond the point of faith-based assertion (i.e. it can't be physically evidenced). Inferior because their brains are incapable of certain nuances of human moral and emotional understanding, possibly -- but that's a different argument, one I don't think we've yet heard as such from Colonial society.