The reason for the uproar wasn't so much that flat-rate pricing is a problem, but that the company switched the API functions that were previously global across any pricing plan to the $199/month plan. So even if you could justify $50/month or $100/month for their service, you didn't have the option. You already implemented the API and can only keep using that implementation with the $200/month service.
I don't even pay my payment gateway $200/month, and they do automated recurring billing and credit card data storage too.
At the same time, the competing subscriptions-as-a-service startups already offered flat rate pricing. The per-transaction pricing Recurly offered was their main differentiator to some of these alternatives. That's the reason so many bootstrappers chose them, so switching to a $200/month fixed cost with zero notice (time to switch) and no grandfathering was a hit right to their primary customer base.
Of course I can't say for sure that's who most of their users are, but the fact that they've now backpedaled again, removed their pricing page entirely and started apologizing to users seems to indicate it wasn't a good move for them.