I'm guessing you already knew the meaning of rather than (as others said, it means instead of), but you're confused by the context in this sentence:
Adam in his five years had absorbed rather than learned never to wonder about an order.
If my hunch is correct, this is really a question about the difference between absorbed and learned in this context. In other words, what does it mean to absorb, rather than learn?
In this context, I would say that absorbing implies a level of learning that is deeper than mere learning. A synonym I would suggest is internalize. From NOAD:
internalize (verb) make (attitudes or behavior) part of one's nature by learning or unconscious assimilation.
So, the author is saying that Adam's ability to not wonder about an order has gone deeper than mere learning. Learning would have implied someone said, "Never wonder about an order!" and Adam responded by saying, "Yes, sir!" and thinking, "Okay, I can understand that." Internalizing, though, would be deeper than that; it would have become second nature to not wonder about an order. In other words, Adam has had enough experience to not wonder – not just because someone told him not to, but because he's come to recognize how pointless it would be to do so – it's become automatic.
As I read the sentence, I guess that Adam, in his five years of service, probably did wonder about orders early in his career. However, time after time after time, such wondering did little good – the orders were still issued, no matter how little sense they seemed to make. Without even knowing it, Adam had absorbed – rather than learned – to not wonder about orders anymore. Wondering would only lead to frustration, so it was much easier to just obey, rather than try to figure out why.