It's that situation where a single structured User object would "foil-out" to like 10 de-normalized tables. It feels ridiculous. It often is a bit ridiculous. Also, I'm not sure how much Open Source RDBMS have improved in the last 8 years, but I know for a fact that MySQL used to just melt under joins like that with any serious load.
As far as the recent OS RDBMS JSON additions, they're just that - recent additions. They feel tacked on. They're treated differently then first-level values. Support in ORMs is lacking. It's hard to find examples online. They're not nearly as easy to use and well supported as hierarchical data is in systems build around it from the ground up (of course).
As far as why MongoDB... because it's the most popular solution. If you hit a problem, someone had probably hit it before, and you can probably find some material online. The leading drivers and libraries are relatively mature and widely used. It makes it a much safer bet as far as tractability of issues you will hit.
I don't really like MongoDB, but the case for using it seems pretty strait-forward to me.