As Brian said, "upset" can refer to several different negative emotions. If you see a small child crying, you might ask the child why he/she is upset. It doesn't always mean "angry."
Literally, to "upset" something is to topple it or turn it over (usually with a negative result). For example, if you "upset" a glass of water, you knock it over, and it spills. So if your emotions are "upset," they have been turned over, or turned to the wrong direction. That could mean that you're angry, or it could mean that you're having some other negative emotion.