How so? In our case, meta data like the userid, browser agent, date entered, etc was always added to the object before it was stored and those fields were indexed. They are just name value pairs.
If you can know for sure from the start that you'll never need queries like this, then of course something like Mongo will be awesome. But requirements change, hence this article.
At another company where I worked where we used Postgres, we had a multitenant set up where each of our (large) customers had their own database. The issue would have been the same.
You would no more “scan over all of your data” with Mongo with indexed fields than you would with an RDMS with indexes.
As requirements change, you do need to migrate your data into a schema that makes sense and that's regardless of whether you're using SQL or MongoDB.
In fact, if you are using C#. You could use the same LINQ syntax either way.