For a little while DS would only drink milk from a bottle, not from a cup. He drank juice from a cup just fine. Then he slowly figured it out. Then, when we started weaning him off of bottles at 18 months, he stopped again, I think out of protest because I tried giving him a cup before bed.
Time to admit my bad mom moment: I let him have chocolate milk a few times as a way to make sure he was getting calcium. Also because I had some at home since it's been a pregnancy craving of mine.
It took about a week, but he got over it. It probably helped that he only gets milk at daycare, so he warmed up to it again. I think it's just a phase.