I don't see the problem with charging for providing a valuable service. If Coursera is valuable then of course the people who contribute their time to making it so deserve to profit from their efforts. If it isn't valuable, then why does it matter what they charge?
I totally agree with what you're saying. However, I'd like to point out that the initial intention with MOOCs was to lower barriers to entry for low income learners around the world. Adding a fee to certificates may have increased barriers to entry in jobs that require certificates now. This, too, may prove to be a trend for increasing charges in MOOCs ... who knows maybe in a few years you'll be paying a massive sum of money to take a course course.
The change is not in charging for value, it's in removing the value from the alternative. It's got some equivalence to a company with dual licensing open source software crippling the community edition in order to sell more of the commercial edition.
