Any science has to live with the
terminology handed down by those who nurtured it in its youth.
Biology is certainly no exception, and is riddled with terms that can be vague, confusing and even harmful.
One such word is 'Mutation' which has connotations of mutants and radioactive waste (and possibly superpowers, depending on). This is because biology is rooted in disease and illness - not just a colourful metaphor. One of the most important things to know about the body is what happens when it goes wrong. So those mutations that lead to disease were the first to be noticed and recorded; leading to a pejorative flavour for the word.
So, are all mutations harmful? This is a question beloved of creationists because it implies the answer 'yes'. This veiwpoint has organisms so finely balanced that any change will 'wreak havoc' on the carefully designed structure. Considering the huge range of disorders that are afflict upon us by our genes, this fear of change is unsurprising.
This leaves a minor problem; why aren't we all the same? I have often noticed the dissimilarity between me and my neighbours (no, not because I'm a twisted, mutant mad scientist...). If any change to the 'blueprints' of a human leads to disease, how can you have more than one variation? Also, I will reluctantly admit that there are those who are genetically better at some things than me - olympic runners with more leg muscle fibers for example. It seems reasonable, therefore for my children to 'mutate' into athletes.
There does not seem to be any difference between variation in a species and mutation. What must be recognised is that change is not intrinsically good or bad - it must be taken in context of the whole system. It so happens that biosystems are adept at managing change - by design. Whether you consider the design to be blind or not is your choice.