As far as I recall (and I've been a Trello user nearly since it was released), it wasn't necessarily Fog Creek's intention to build a huge monetized business out of Trello.
In fact, at some point, users started to get anxious that Trello was free and actually WANTED to throw money at the company. I suppose part of that was the perception that if you're paying for it, it will be more likely to survive and won't go away? This was what spurred Trello to create an offering of something (via Trello Gold) - simply so people could pay for something they liked and feel good about themselves, and get something in return.
Actually, I don't know this for sure, but I think they genuinely built Trello because it was a tool that they really felt should exist, and wanted to make it work as inexpensively as they could and support as many as they could, while staying permanently free. I think Trello was an experiment for them, one which succeeded at gaining the huge userbase with a simple tool (which I believe was their goal).
Once the realization that the huge userbase itself was valuable, it was inevitable that someone would buy it out. Atlassian wanted to be associated with that huge userbase, to help with Jira... maybe or maybe not to actually bring Trello into the fold with their existing products.
In any case, Trello is a huge accomplishment, before the buyout, and as a business, even moreso afterwards. I was thinking about building (and actually working on) something like Trello before it existed, but I didn't necessarily think the world needed something so simple. I would have been quite happy with this result!!! They made an absolute ton of users (self included) very happy with the results of their labor, and now they have a wonderful reward from it.
Trello did not fail to build a $1B+ business. Trello succeeded at building a $425M business through good faith and hard work. Bravo.