God's ethics are on a different scale then our human ones. Our sense of ethics revolves around personal safety, individual freedom and social consent. Our ideas of justice and fairness are also derived from these. Since God does not operate from such a basis, it is easy to see why God might not be just according to our expectations.
God is about divine balance, not human justice. The idea of 'balance' is somewhat intertwined with the idea of 'moderation'. If we see a line with the two extremes at each and, sometimes we are quick to judge that the point of balance lies in the middle. It may be a point of average moderation, but balance? Balance can lie anywhere along the line, at more points than one.
God cannot be just or fair for the simple reason that God doesn't see things as 'good' and 'bad', therefore it's not about balancing out one with the other on some cosmic scale. It's an exaggeration to say that God doesn't care or is unfair - such limited human concepts simply don't enter the equation.
God is just in the sense that everything is God, and any 'injustice' that is done is done to God. For God, karma is not a slow turning wheel that sometimes hits and sometimes misses, but it is instant and complete. The wrongdoer and the victim are one in God - what you do to another, you do it to yourself. If you try to get around this by limiting your awareness to a lower level and thus avoid responsibility, you may succeed, but being in such a state is already an effect instant karma.
Is God just? Look for balance, not justice.