A bit late to help the OP, but I will leave this answer in the hope that it can help someone.
I do not know about other versions, but using select2-rails 3.5.9.3 (which according to their github page means version 3.5 is used select2) I was able to change the background color only as follows:
.select2-choice { background-color: #00f !important; }
The selector mentioned by Matthew for the results works.
Anyway, I have not tried using "vanilla select2", so I do not know if there is a difference in this case.
Grandor
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