An affliction makes you suffer, but you have to deal with it anyway. Diseases are often said to be afflictions, but the word can mean just about anything that causes great suffering.
The word afflict, which makes up the first part of the word, means to cause this type of trouble. "Tom liked to inflict pain on his brother. His brother considered Tom just one more affliction he had to bear." The word can also be used as an exaggeration of something that isn't so bad––"Homework is often seen as an affliction by students and parents alike."