I agree that this situation is both tragic and depressingly, probably avoidable, although it is worth pointing out that the rate is just over one in ten thousand for the worst airline (United) or two in 100,000 for the best (Alaska).
From my reading, unfortunately causes seem relegated to anecdata in this case as only rates are officially recorded. Reading anecdotes, however, the issues also seem to mostly be related to ground-handling and packaging issues, between animals which are not properly crated (much as the human in the article seems to have been improperly crated!) or are heartbreakingly left on the tarmac for extended timeframes during harsh weather.