Should you pay for a MOOC-based certification in R?

My simple response is no. Instead, you should use the portfolio you create as part of your learning to aggressively market yourself to people who care about the kinds of things you can do for them. That's where you will get the payoff, and it's the only proof that really matters.

This said, I have occasionally paid for certifications. Why don't MOOCs teaching R, even very good ones, pass the test?

• Paying does not entitle you to premium support or any support really. At most, it seems you pay just to guarantee that it's really you taking the course although, to be fair, this verification may itself have some incidental value. For instance one study group of students taking Coursera's Data Science Specialization use whether you are a paying, identity-verified course participant, as one criterion for joining them. If that's important to you, then paying might be worth it.
• Employers don't really value certification unless the field is well understood and the certification tests can be used to differentiate ability in the market place. Learning R is of some value, but it's really being able to structure problems and derive useful answers that is the real value. MOOCs don't teach that, and MOOC certifications don't demonstrate you can do that.
• The quality of MOOCs is uneven. For instance, even the excellent MITx MOOC I'm currently auditing, The Analytics Edge, has some glaring mistakes in one of the problem sets. If you've taken enough courses on quantitative analysis, you know that mistakes are bound to happen. The problem is that you have no real recourse other than complaining on the forums. Why pay for that?

So, in short, I say don't pay because it doesn't get me anything. When might I pay? If I could pay $300 or $400 and get real support, I'd consider it for certain topics. I might (and have) paid several thousand dollars for learning experiences that then give me access to verifiable earning opportunities. I've also paid up to $1000 for subscriptions to services that provide real analytic value.