It is not just referring to money. It means that at the end of a time, or of doing something, you have a change, or a result. Examples. After attending the opera, she came away with a better appreciation of music. After spending time on a farm, we come away with a love of nature

'Come away with' means what you got from something. It can be used in that sentence, because you are saying what you took away (an end of year bonus). It can be used to say what you got from someone or an expeirence. Example: I will come away with a puppy; We usually come away with knowledge. 'Come away' is a verb and 'with' is a helping verb.

It generally refers to something unexpected. If you come away with an end of year bonus, it really means that you started the year without the promise of a bonus, but you performed so well, you actually got on. Example: China played Japan and came away with a draw. (Japan were expected to win) Four years ago Britain came away with a lot of gold medals. (Britain had before then never shone at the Olympics) So, "come away with" can refer to any unexpected result, not just money!