Pretty well justified, actually. We didn't really have solid understanding of how diseases spread, or even what they were, until relatively recently. An effort has been made to find out, and as much as we make fun of medieval humours today, the theory did describe the symptoms somewhat accurately, but there simply wasn't the necessary equipment to arrive at the correct answer.

For example, a prevailing theory of Black Death of 14th century was that an invisible cloud of toxic mist was sweeping the land. They identified that there were three versions of the disease, but that's about the limit of what they could do.

For further reading, research a little something called the Sanitation movement - it's basically the thing that gave us modern hygiene, including among other things, proper sewage disposal systems. And there are cool moments there, like straight up lifting city blocks to build sewers under them: http://factually.gizmodo.com/chicago-was-raised-more-than-4-feet-in-the-1800s-to-bui-1646409024