Look at it from the "average bootstrapper"'s perspective (whatever that is). They needed a recurring billing system, looked around, found one that was good because of its free plan (fully intending to pay as soon as they got enough users to cover the costs). After choosing Chargify on the promise of their free tier, they then spent 1000s of hours of work to integrate it.
Now, I'm not saying Chargify necessarily owes them for their development costs. But there is an implied contract: I'll implement Chargify's api and start working with them until I make enough money to pay, and as soon as I do, I'll start paying. This was the point of Chargify's free tier, and was probably advertised as such. I can understand why people are upset.