Humankind has the unfortunate capability to divide the world into "us" and "them," and that ability isn't going to evolve away anytime soon. Maybe it came from our early tribal existence; it would have been imperative for you as a member of your tribe to be concerned with the tribe; anything that threatened or competed with your tribe was, by definition, a threat.
It may also have to do with our ability to group things together; it would be quite easy to segregate another group because they do things differently than me or mine. Stereotypes arose because they were convenient methods of grouping and differentiating.
Of course, the problem then comes when a member of another grouping does not conform to the suppositions we've imposed upon that group; rather than treating people as individuals with their own characteristics, we see them merely as members of an opposing group, which all share the same general characteristics, which are not the same general characteristics that our group shares.
Are stereotypes bad? Only when they negate individuality, and they appear to do that by definition; it may be more helpful to treat stereotypes as a generalized, frequently inaccurate representation of characteristics of another group, to which some individual may or may not conform.