There are different perceptions of the Space Jockeys. I have read about how they are benevolent and hope to meet mankind under better circumstances.....but they are also shown to be malevolent, perhaps even ambivalent. Considering that these are supposedly godlike entities, it's realistic to assume that since they have a higher technological capability and a higher level of intelligence, they wouldn't need to take their creations' well-being or interests to heart.
As for the Space Jockey being something subordinate......well, damn. That reminds me of the issue of "what created that which created that which created that which created that which created that which created that which created that which created that which created that which created God," that sort of thing. I'm sure that since the Space Jockeys are a physical, sentient species, they probably believe in some higher power of sorts, some celestial entity that just [i]is[/i] (kind of like how we humans perceive God).
I ordered Alien: Vault a few days ago at Barnes & Noble, and I'm looking forward to receiving it so I can dig into it......there was a copy available there, but once I noticed that the book is chock-full of little pieces of paper and what-not, I distrusted that it had everything, so I'm hoping for a fresh copy soon.