I'll use the USA as context for the answer. As this is a volatile period of time for what was traditionally considered "minority" (homosexuals, transgenders) and in light of recent race tensions resulting from police-involved shootings, the definition of this word and the feelings surrounding it may change rapidly.
Statistical and anthropological arguments can be made against the use of "minority" as a descriptive word. Traditionally it has been used to describe "non-whites" in this country. However, is that still the case considering the high volume of "non-white" people in the country now? Furthermore, the use of race terms (white, black, Asian, Hispanic) is quickly becoming considered in anthropological academic circles to be arbitrary (is someone from Egypt black? What about native Haitians? How far north in China do you have to go before you are no longer surrounded by an "Asian" populace? Are Indians "Asians?")
In short, as with many controversial words, "minority" is as offensive as you desire it to be based on the context you are using it in. Typically I would say no, it is not offensive, and is probably your best choice of word to use when referring to non-members of whatever homogeneous culture/race/etc which you are discussing. Today, it will be important to define what exactly "minority" is, especially if you are charting data, as in the USA this is no longer immediately clear.